diff --git a/.github/workflows/test_playbook.yaml b/.github/workflows/test_playbook.yaml
index 87c9cf3..b5fb4f4 100644
--- a/.github/workflows/test_playbook.yaml
+++ b/.github/workflows/test_playbook.yaml
@@ -39,10 +39,10 @@ jobs:
         python3 -m pip install -U pip setuptools
 
 
-    - name: Install ansible 2.10.1 and bioblend in ubuntu 20.04
+    - name: Install ansible 3.0 and bioblend in ubuntu 20.04
       run: |
-        python3 -m pip install ansible==2.10.1
-        python3 -m pip install --ignore-installed https://github.com/galaxyproject/bioblend/archive/refs/tags/v1.0.0.zip pytest
+        python3 -m pip install ansible==3.0
+        python3 -m pip install --ignore-installed https://github.com/galaxyproject/bioblend/archive/refs/tags/v1.2.0.zip pytest
     
     - name: Display pip python and ansible settings
       run: |
@@ -73,10 +73,12 @@ jobs:
                          --skip-tags galaxy_build_client \
                          playbook.yml
 
-    - name: Sleep for 15 seconds and check galaxyctl status
+    - name: Sleep for 30 secs and check galaxyctl status
       run: |
-        echo "waiting 15 sec" && sleep 15
-        sudo su - galaxy -c "source galaxy/.venv/bin/activate && galaxyctl status"
+        sudo galaxyctl graceful
+        echo "waiting 30 sec" && sleep 30
+        sudo galaxyctl status
+# sudo su - galaxy -c "source galaxy/.venv/bin/activate && galaxyctl status"
 
     - name: check Galaxy API is alive
       run: |
diff --git a/.gitignore b/.gitignore
index 044549a..5ae703f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,142 +2,10 @@
 .DS_Store
 *.pyc
 docs/html
-
-roles/ansible-slurm/
-roles/galaxyproject.galaxy/
-roles/galaxyproject.nginx/
-roles/galaxyproject.postgresql/
-roles/galaxyproject.postgresql_objects/
-roles/geerlingguy.pip/
-roles/uchida.miniconda/
-roles/install.galaxy-tools/
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
+.vault-password.txt
+roles/galaxyproject.galaxy
+roles/galaxyproject.miniconda
+roles/galaxyproject.nginx
+roles/galaxyproject.postgresql
+roles/galaxyproject.postgresql_objects
+roles/galaxyproject.slurm
diff --git a/Dockerfile.galaxyxpand b/Dockerfile.galaxyxpand
index 5060342..c1236b6 100644
--- a/Dockerfile.galaxyxpand
+++ b/Dockerfile.galaxyxpand
@@ -17,7 +17,7 @@ RUN apt update && \
     postgresql-12 postgresql-client-12 postgresql-contrib-12 \
     locales dirmngr && apt clean
 
-RUN python3 -m pip install -U pip && python3 -m pip install ansible==2.10.7 && \
+RUN python3 -m pip install -U pip && python3 -m pip install ansible==3.0 && \
     python3 -m pip install -U cryptography pyyaml
 
 # Run the rest of the commands as the ``postgres`` user created by the ``postgres-12``
@@ -37,7 +37,9 @@ USER postgres
 
 RUN    /etc/init.d/postgresql start &&\
     psql --command "CREATE USER root WITH SUPERUSER PASSWORD 'galaxy';" && \
-    createdb -O root rootdb
+    createdb -O root rootdb && \
+    psql --command "CREATE USER galaxy WITH PASSWORD 'galaxy';" && \
+    createdb -O galaxy galaxy
 
 # Adjust PostgreSQL configuration so that remote connections to the
 # database are possible.
@@ -80,11 +82,16 @@ WORKDIR /setup
 ENV LC_ALL=en_US.UTF-8 \
     LANG=en_US.UTF-8
 
+# in next step, a faulty handler that triggered systemctl is deleted
+# before running the playbook
+
 RUN echo "remote_tmp = /setup/.ansible/tmp" >> ansible.cfg && \
     service postgresql start && \
     sed -i '/slurm-wlm/d' playbook.yml && sed -i '/slurm-drmaa-dev/d' playbook.yml && \
     ansible-galaxy install -r requirements.yml -p roles -f && \
-    ansible-playbook -i environments/Docker/hosts -c local playbook.yml
+    head -n -4 roles/galaxyproject.galaxy/handlers/main.yml > tmp.txt &&\
+    mv tmp.txt roles/galaxyproject.galaxy/handlers/main.yml &&\
+    ansible-playbook -i environments/Docker/hosts playbook.yml
 
 ONBUILD  WORKDIR  /setup
 ONBUILD  COPY  .  /setup
diff --git a/ansible.cfg b/ansible.cfg
index f56d402..943192c 100644
--- a/ansible.cfg
+++ b/ansible.cfg
@@ -1,8 +1,12 @@
 [defaults]
 interpreter_python = /usr/bin/python3
 inventory = ./environments/dev_gce/hosts
-retry_files_enabled = False
-display_skipped_hosts = False
-stdout_callback = community.general.yaml
-bin_ansible_callbacks = True # Use the stdout_callback when running ad-hoc commands.
+# Use the YAML callback plugin.
+stdout_callback = yaml
+# Use the stdout_callback when running ad-hoc commands.
+bin_ansible_callbacks = True
 # vault_password_file = ../ansible_vault_password
+
+# Show diffs of changes
+[diff]
+always = True
diff --git a/environments/000_cross_env_vars b/environments/000_cross_env_vars
index 6a2a681..0174a1e 100644
--- a/environments/000_cross_env_vars
+++ b/environments/000_cross_env_vars
@@ -1,29 +1,17 @@
 ---
 # Python 3 support
-pip_virtualenv_command: /usr/bin/python3 -m virtualenv
-pip_package: python3-pip
+pip_virtualenv_command: /usr/bin/python3 -m venv
 
-# PostgreSQL
-postgresql_objects_users:
-  - name: galaxy
-postgresql_objects_databases:
-  - name: galaxy
-    owner: galaxy
-# PostgreSQL Backups
-postgresql_backup_dir: /data/backups
-postgresql_backup_local_dir: "{{ '~postgres' | expanduser }}/backups"
+# Common variables needed by all hosts
+galaxy_user_name: galaxy
+galaxy_db_name: galaxy
 
-# galaxy
-galaxy_config_perms: 0664
 
-# when transitionning from galaxykickstart to galaxyXpand set to 'yes'
-galaxykickstart_to_gravity: no
+# galaxy (check requirement)
+galaxy_config_perms: 0664
 
 # to install uptime set to 'yes'
 install_uptime: no
 
-# to not install postgresql set to 'no"
-install_postgresql: yes
-
 # to not install slurm set to 'no'
 install_slurm: yes
diff --git a/environments/ARTbio/files/galaxy/config/artbio_tool_list.yml b/environments/ARTbio/files/galaxy/config/artbio_tool_list.yml
index 7b4eb7f..4f79c71 100644
--- a/environments/ARTbio/files/galaxy/config/artbio_tool_list.yml
+++ b/environments/ARTbio/files/galaxy/config/artbio_tool_list.yml
@@ -1,36 +1,31 @@
 tools:
-- name: yac_clipper
-  owner: artbio
-  tool_panel_section_id: mississippi_tool_suite
-  tool_panel_section_label: Mississippi Tool Suite
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: small_rna_signatures
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sr_bowtie_dataset_annotation
+- name: sr_bowtie
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: small_rna_maps
+- name: yac_clipper
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fasta_merge_files_and_filter_unique_sequences
-  owner: galaxyp
+- name: sr_bowtie_dataset_annotation
+  owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bamparse
+- name: small_rna_maps
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sr_bowtie
-  owner: artbio
+- name: fasta_merge_files_and_filter_unique_sequences
+  owner: galaxyp
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -44,11 +39,6 @@ tools:
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: justdiff
-  owner: artbio
-  tool_panel_section_id: mississippi_tool_suite
-  tool_panel_section_label: Mississippi Tool Suite
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: msp_sr_size_histograms
   owner: drosofff
   tool_panel_section_id: mississippi_tool_suite
@@ -59,7 +49,7 @@ tools:
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fetch_fasta_from_ncbi
+- name: cap3
   owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
@@ -84,31 +74,21 @@ tools:
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blastparser_and_hits
-  owner: artbio
+- name: bowtie2
+  owner: devteam
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: cap3
+- name: blastx_to_scaffold
   owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: concatenate_multiple_datasets
+- name: blastparser_and_hits
   owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bowtie2
-  owner: devteam
-  tool_panel_section_id: metavisitor
-  tool_panel_section_label: Metavisitor
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: regex_find_replace
-  owner: galaxyp
-  tool_panel_section_id: metavisitor
-  tool_panel_section_label: Metavisitor
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: get_orfs_or_cdss
   owner: peterjc
   tool_panel_section_id: metavisitor
@@ -134,11 +114,6 @@ tools:
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: msp_cap3
-  owner: drosofff
-  tool_panel_section_id: metavisitor
-  tool_panel_section_label: Metavisitor
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: concatenate_multiple_datasets
   owner: mvdbeek
   tool_panel_section_id: metavisitor
@@ -154,16 +129,6 @@ tools:
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blast_to_scaffold
-  owner: drosofff
-  tool_panel_section_id: metavisitor
-  tool_panel_section_label: Metavisitor
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fastq_to_fasta
-  owner: devteam
-  tool_panel_section_id: metavisitor
-  tool_panel_section_label: Metavisitor
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: yac_clipper
   owner: drosofff
   tool_panel_section_id: metavisitor
@@ -174,67 +139,242 @@ tools:
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blast_unmatched
-  owner: artbio
-  tool_panel_section_id: metavisitor
-  tool_panel_section_label: Metavisitor
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blastx_to_scaffold
-  owner: artbio
-  tool_panel_section_id: metavisitor
-  tool_panel_section_label: Metavisitor
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: srnapipe
   owner: brasset_jensen
   tool_panel_section_id: mississippi_extra_tools
   tool_panel_section_label: Mississippi Extra Tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: justgzip
-  owner: artbio
-  tool_panel_section_id: mississippi_extra_tools
-  tool_panel_section_label: Mississippi Extra Tools
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mismatch_frequencies
   owner: mvdbeek
   tool_panel_section_id: mississippi_extra_tools
   tool_panel_section_label: Mississippi Extra Tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: exomedepth
-  owner: crs4
+- name: strelka_germline
+  owner: iuc
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcf2tsv
+- name: snvtocnv
+  owner: artbio
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: plink
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: snpeff
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_norm
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_cnv
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_consensus
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_counts
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_fill_an_ac
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_fill_tags
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_fixploidy
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_frameshifts
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_impute_info
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_mendelian
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_missing2ref
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_setgt
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_tag2tag
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_reheader
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_roh
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_dosage
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_plugin_color_chrs
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_merge
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_isec
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_gtcheck
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_csq
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_convert_to_vcf
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_convert_from_vcf
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_concat
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_call
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_annotate
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: vcfvcfintersect
   owner: devteam
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deepvariant
+- name: freebayes
+  owner: devteam
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_filter
   owner: iuc
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: snpsift
+- name: bcftools_view
   owner: iuc
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcfallelicprimitives
+- name: samtools_mpileup
   owner: devteam
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcfcombine
+- name: bcftools_mpileup
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: vcf2maf
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: mutational_patterns
+  owner: artbio
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: lofreq_call
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: lumpy_smoove
+  owner: artbio
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: exomedepth
+  owner: crs4
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: vcf2tsv
   owner: devteam
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: snpeff
+- name: deepvariant
   owner: iuc
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: freebayes
+- name: snpsift
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: vcfallelicprimitives
+  owner: devteam
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: vcfcombine
   owner: devteam
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
@@ -264,6 +404,21 @@ tools:
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_stats
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_query_list_samples
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bcftools_query
+  owner: iuc
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: table_annovar
   owner: devteam
   tool_panel_section_id: genomic_variants
@@ -279,11 +434,6 @@ tools:
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: lumpy_smoove
-  owner: artbio
-  tool_panel_section_id: genomic_variants
-  tool_panel_section_label: Genomic Variants
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: delly_call
   owner: iuc
   tool_panel_section_id: genomic_variants
@@ -304,6 +454,21 @@ tools:
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: add_value
+  owner: devteam
+  tool_panel_section_id: textutil
+  tool_panel_section_label: Text Manipulation
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: justdiff
+  owner: artbio
+  tool_panel_section_id: textutil
+  tool_panel_section_label: Text Manipulation
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: add_column_headers
+  owner: estrain
+  tool_panel_section_id: textutil
+  tool_panel_section_label: Text Manipulation
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: regex_find_replace
   owner: galaxyp
   tool_panel_section_id: textutil
@@ -349,11 +514,6 @@ tools:
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: unique
-  owner: bgruening
-  tool_panel_section_id: textutil
-  tool_panel_section_label: Text Manipulation
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: replace_column_by_key_value_file
   owner: bgruening
   tool_panel_section_id: textutil
@@ -364,16 +524,6 @@ tools:
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sampline
-  owner: xuebing
-  tool_panel_section_id: textutil
-  tool_panel_section_label: Text Manipulation
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: add_value
-  owner: devteam
-  tool_panel_section_id: textutil
-  tool_panel_section_label: Text Manipulation
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: tables_arithmetic_operations
   owner: devteam
   tool_panel_section_id: textutil
@@ -394,12 +544,22 @@ tools:
   tool_panel_section_id: group
   tool_panel_section_label: Join, Subtract and Group
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: crossmap_vcf
-  owner: iuc
+- name: justgzip
+  owner: artbio
   tool_panel_section_id: convert
   tool_panel_section_label: Convert Formats
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_cram_to_bam
+- name: bigwig_to_bedgraph
+  owner: artbio
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: agat
+  owner: bgruening
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: crossmap_vcf
   owner: iuc
   tool_panel_section_id: convert
   tool_panel_section_label: Convert Formats
@@ -439,6 +599,11 @@ tools:
   tool_panel_section_id: convert
   tool_panel_section_label: Convert Formats
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: samtools_cram_to_bam
+  owner: iuc
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: dna_protein_transle
   owner: jasper
   tool_panel_section_id: convert
@@ -519,6 +684,21 @@ tools:
   tool_panel_section_id: fetch_sequences
   tool_panel_section_label: Fetch Sequences
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: fastqc
+  owner: devteam
+  tool_panel_section_id: ngs:_qc_and_manipulation
+  tool_panel_section_label: 'NGS: QC and manipulation'
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: seq_filter_by_id
+  owner: peterjc
+  tool_panel_section_id: ngs:_qc_and_manipulation
+  tool_panel_section_label: 'NGS: QC and manipulation'
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: multiqc
+  owner: iuc
+  tool_panel_section_id: ngs:_qc_and_manipulation
+  tool_panel_section_label: 'NGS: QC and manipulation'
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: mapping_quality_stats
   owner: artbio
   tool_panel_section_id: ngs:_qc_and_manipulation
@@ -549,16 +729,6 @@ tools:
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fastqc
-  owner: devteam
-  tool_panel_section_id: ngs:_qc_and_manipulation
-  tool_panel_section_label: 'NGS: QC and manipulation'
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: multiqc
-  owner: iuc
-  tool_panel_section_id: ngs:_qc_and_manipulation
-  tool_panel_section_label: 'NGS: QC and manipulation'
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: fastq_paired_end_deinterlacer
   owner: devteam
   tool_panel_section_id: ngs:_qc_and_manipulation
@@ -569,11 +739,6 @@ tools:
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: artbio_bam_cleaning
-  owner: artbio
-  tool_panel_section_id: ngs:_qc_and_manipulation
-  tool_panel_section_label: 'NGS: QC and manipulation'
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: trinity_align_and_estimate_abundance
   owner: iuc
   tool_panel_section_id: ngs:_assembly
@@ -659,7 +824,7 @@ tools:
   tool_panel_section_id: ngs:_assembly
   tool_panel_section_label: 'NGS: Assembly'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bwa_mem2
+- name: kallisto_quant
   owner: iuc
   tool_panel_section_id: ngs:_mapping
   tool_panel_section_label: 'NGS: Mapping'
@@ -669,11 +834,21 @@ tools:
   tool_panel_section_id: ngs:_mapping
   tool_panel_section_label: 'NGS: Mapping'
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: artbio_bam_cleaning
+  owner: artbio
+  tool_panel_section_id: ngs:_mapping
+  tool_panel_section_label: 'NGS: Mapping'
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: hisat2
   owner: iuc
   tool_panel_section_id: ngs:_mapping
   tool_panel_section_label: 'NGS: Mapping'
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bwa_mem2
+  owner: iuc
+  tool_panel_section_id: ngs:_mapping
+  tool_panel_section_label: 'NGS: Mapping'
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: rsem
   owner: artbio
   tool_panel_section_id: ngs:_mapping
@@ -714,11 +889,6 @@ tools:
   tool_panel_section_id: ngs:_rna_analysis
   tool_panel_section_label: 'NGS: RNA Analysis'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: featurecounts
-  owner: iuc
-  tool_panel_section_id: ngs:_rna_analysis
-  tool_panel_section_label: 'NGS: RNA Analysis'
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: htseq_count
   owner: lparsons
   tool_panel_section_id: ngs:_rna_analysis
@@ -729,21 +899,11 @@ tools:
   tool_panel_section_id: ngs:_rna_analysis
   tool_panel_section_label: 'NGS: RNA Analysis'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: cpm_tpm_rpk
-  owner: artbio
-  tool_panel_section_id: ngs:_rna_analysis
-  tool_panel_section_label: 'NGS: RNA Analysis'
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: rsem
   owner: artbio
   tool_panel_section_id: ngs:_rna_analysis
   tool_panel_section_label: 'NGS: RNA Analysis'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deseq2_normalization
-  owner: artbio
-  tool_panel_section_id: ngs:_rna_analysis
-  tool_panel_section_label: 'NGS: RNA Analysis'
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: cuffnorm
   owner: devteam
   tool_panel_section_id: ngs:_rna_analysis
@@ -764,6 +924,31 @@ tools:
   tool_panel_section_id: ngs:_rna_analysis
   tool_panel_section_label: 'NGS: RNA Analysis'
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: samtools_cram_to_bam
+  owner: iuc
+  tool_panel_section_id: ngs:_sam_tools
+  tool_panel_section_label: 'NGS: SAM Tools'
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sambamba
+  owner: artbio
+  tool_panel_section_id: ngs:_sam_tools
+  tool_panel_section_label: 'NGS: SAM Tools'
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: samtools_reheader
+  owner: devteam
+  tool_panel_section_id: ngs:_sam_tools
+  tool_panel_section_label: 'NGS: SAM Tools'
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: ngsutils_bam_filter
+  owner: iuc
+  tool_panel_section_id: ngs:_sam_tools
+  tool_panel_section_label: 'NGS: SAM Tools'
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bamtools
+  owner: devteam
+  tool_panel_section_id: ngs:_sam_tools
+  tool_panel_section_label: 'NGS: SAM Tools'
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: samtools_flagstat
   owner: devteam
   tool_panel_section_id: ngs:_sam_tools
@@ -804,7 +989,7 @@ tools:
   tool_panel_section_id: ngs:_sam_tools
   tool_panel_section_label: 'NGS: SAM Tools'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sambamba
+- name: bamparse
   owner: artbio
   tool_panel_section_id: ngs:_sam_tools
   tool_panel_section_label: 'NGS: SAM Tools'
@@ -814,11 +999,6 @@ tools:
   tool_panel_section_id: ngs:_sam_tools
   tool_panel_section_label: 'NGS: SAM Tools'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_mpileup
-  owner: devteam
-  tool_panel_section_id: ngs:_sam_tools
-  tool_panel_section_label: 'NGS: SAM Tools'
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: sambamba_filter
   owner: lomereiter
   tool_panel_section_id: ngs:_sam_tools
@@ -859,11 +1039,6 @@ tools:
   tool_panel_section_id: ngs:_sam_tools
   tool_panel_section_label: 'NGS: SAM Tools'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bamtools
-  owner: devteam
-  tool_panel_section_id: ngs:_sam_tools
-  tool_panel_section_label: 'NGS: SAM Tools'
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: intersect
   owner: devteam
   tool_panel_section_id: bxops
@@ -909,6 +1084,11 @@ tools:
   tool_panel_section_id: bxops
   tool_panel_section_label: Operate on Genomic Intervals
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: picard_plus
+  owner: devteam
+  tool_panel_section_id: picard_tools
+  tool_panel_section_label: Picard Tools
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: picard
   owner: devteam
   tool_panel_section_id: picard_tools
@@ -919,12 +1099,22 @@ tools:
   tool_panel_section_id: ncbi_blast+
   tool_panel_section_label: NCBI BLAST+
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: kallisto_pseudo
+- name: sleuth
   owner: iuc
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: kallisto_quant
+- name: annotatemyids
+  owner: iuc
+  tool_panel_section_id: differential_expression
+  tool_panel_section_label: Differential Expression
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: goseq
+  owner: iuc
+  tool_panel_section_id: differential_expression
+  tool_panel_section_label: Differential Expression
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: ruvseq
   owner: iuc
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
@@ -934,6 +1124,11 @@ tools:
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: kallisto_pseudo
+  owner: iuc
+  tool_panel_section_id: differential_expression
+  tool_panel_section_label: Differential Expression
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: dexseq
   owner: iuc
   tool_panel_section_id: differential_expression
@@ -954,11 +1149,6 @@ tools:
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: ruvseq
-  owner: iuc
-  tool_panel_section_id: differential_expression
-  tool_panel_section_label: Differential Expression
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: limma_voom
   owner: iuc
   tool_panel_section_id: differential_expression
@@ -974,11 +1164,6 @@ tools:
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: goseq
-  owner: iuc
-  tool_panel_section_id: differential_expression
-  tool_panel_section_label: Differential Expression
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: trinity_run_de_analysis
   owner: iuc
   tool_panel_section_id: differential_expression
@@ -1004,6 +1189,11 @@ tools:
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: deseq2
+  owner: iuc
+  tool_panel_section_id: differential_expression
+  tool_panel_section_label: Differential Expression
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: rsem
   owner: artbio
   tool_panel_section_id: differential_expression
@@ -1054,8 +1244,8 @@ tools:
   tool_panel_section_id: chip-seq
   tool_panel_section_label: ChIP-seq
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fishertest
-  owner: artbio
+- name: column_maker
+  owner: devteam
   tool_panel_section_id: stats
   tool_panel_section_label: Statistics
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -1124,6 +1314,11 @@ tools:
   tool_panel_section_id: fastx_toolkit
   tool_panel_section_label: fastx toolkit
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: rseqc
+  owner: nilesh
+  tool_panel_section_id: deeptools
+  tool_panel_section_label: DeepTools
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: deeptools_plot_coverage
   owner: bgruening
   tool_panel_section_id: deeptools
@@ -1259,11 +1454,6 @@ tools:
   tool_panel_section_id: plots
   tool_panel_section_label: Graph/Display Data
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: venn_list
-  owner: peterjc
-  tool_panel_section_id: plots
-  tool_panel_section_label: Graph/Display Data
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: heat_map_creation
   owner: md-anderson-bioinformatics
   tool_panel_section_id: plots
@@ -1304,6 +1494,11 @@ tools:
   tool_panel_section_id: artbio_goodies
   tool_panel_section_label: ARTbio Goodies
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: unzip
+  owner: imgteam
+  tool_panel_section_id: collection_operations
+  tool_panel_section_label: Collection Operations
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: bundle_collections
   owner: nml
   tool_panel_section_id: collection_operations
@@ -1314,11 +1509,6 @@ tools:
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: concatenate_multiple_datasets
-  owner: artbio
-  tool_panel_section_id: collection_operations
-  tool_panel_section_label: Collection Operations
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: extract_element_from_collection
   owner: erasmus-medical-center
   tool_panel_section_id: collection_operations
@@ -1334,18 +1524,28 @@ tools:
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: scanpy_inspect
+- name: gsc_scran_normalize
+  owner: artbio
+  tool_panel_section_id: single-cell_analysis
+  tool_panel_section_label: Single-Cell analysis
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: cpm_tpm_rpk
+  owner: artbio
+  tool_panel_section_id: single-cell_analysis
+  tool_panel_section_label: Single-Cell analysis
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: rna_starsolo
   owner: iuc
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: raceid_inspecttrajectory
+- name: scanpy_inspect
   owner: iuc
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_high_dimensions_visualisation
-  owner: artbio
+- name: raceid_inspecttrajectory
+  owner: iuc
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -1369,11 +1569,6 @@ tools:
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_mannwhitney_de
-  owner: artbio
-  tool_panel_section_id: single-cell_analysis
-  tool_panel_section_label: Single-Cell analysis
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: scanpy_filter
   owner: iuc
   tool_panel_section_id: single-cell_analysis
@@ -1394,11 +1589,6 @@ tools:
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_gene_expression_correlations
-  owner: artbio
-  tool_panel_section_id: single-cell_analysis
-  tool_panel_section_label: Single-Cell analysis
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: scanpy_normalize
   owner: iuc
   tool_panel_section_id: single-cell_analysis
@@ -1499,36 +1689,16 @@ tools:
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_center_scale
-  owner: artbio
-  tool_panel_section_id: single-cell_analysis
-  tool_panel_section_label: Single-Cell analysis
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: gsc_signature_score
   owner: artbio
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_filter_cells
-  owner: artbio
-  tool_panel_section_id: single-cell_analysis
-  tool_panel_section_label: Single-Cell analysis
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: datamash_transpose
   owner: iuc
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_cpm_tpm_rpk
-  owner: artbio
-  tool_panel_section_id: single-cell_analysis
-  tool_panel_section_label: Single-Cell analysis
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_filter_genes
-  owner: artbio
-  tool_panel_section_id: single-cell_analysis
-  tool_panel_section_label: Single-Cell analysis
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: anndata_export
   owner: iuc
   tool_panel_section_id: single-cell_analysis
@@ -1549,11 +1719,6 @@ tools:
   tool_panel_section_id: single-cell_analysis
   tool_panel_section_label: Single-Cell analysis
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: rna_starsolo
-  owner: iuc
-  tool_panel_section_id: single-cell_analysis
-  tool_panel_section_label: Single-Cell analysis
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: pygenometracks
   owner: iuc
   tool_panel_section_id: bedtools
@@ -1579,6 +1744,11 @@ tools:
   tool_panel_section_id: graph/display_data
   tool_panel_section_label: Graph/Display Data
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: get_reference_fasta
+  owner: artbio
+  tool_panel_section_id: getext
+  tool_panel_section_label: Get Data
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: show_metadata
   owner: yhoogstrate
   tool_panel_section_id: getext
@@ -1589,11 +1759,6 @@ tools:
   tool_panel_section_id: getext
   tool_panel_section_label: Get Data
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: get_reference_fasta
-  owner: artbio
-  tool_panel_section_id: getext
-  tool_panel_section_label: Get Data
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: extract_genomic_dna
   owner: iuc
   tool_panel_section_id: getext
@@ -1634,203 +1799,38 @@ tools:
   tool_panel_section_id: filter
   tool_panel_section_label: Filter and Sort
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_reheader
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: vcfsort
   owner: devteam
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_missing2ref
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_color_chrs
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_fill_an_ac
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_view
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_mendelian
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_fill_tags
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_tag2tag
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_concat
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_annotate
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_roh
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_fixploidy
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_counts
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_convert_from_vcf
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_setgt
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_isec
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_cnv
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_mpileup
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_frameshifts
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_query_list_samples
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_gtcheck
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_dosage
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_stats
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_csq
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_query
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_norm
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_convert_to_vcf
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_impute_info
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_filter
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_merge
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_call
-  owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_consensus
+- name: medaka_consensus
   owner: iuc
-  tool_panel_section_id: bcftools
-  tool_panel_section_label: BCFtools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: xpore
-  owner: artbio
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: medaka_consensus
-  owner: iuc
-  tool_panel_section_id: ''
-  tool_panel_section_label: ''
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: medaka_consensus_pipeline
-  owner: iuc
-  tool_panel_section_id: ''
-  tool_panel_section_label: ''
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: medaka_variant_pipeline
   owner: iuc
-  tool_panel_section_id: ''
-  tool_panel_section_label: ''
+  tool_panel_section_id: nanopore
+  tool_panel_section_label: Nanopore
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: medaka_variant
   owner: iuc
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: tarfast5
+- name: minimap2
+  owner: iuc
+  tool_panel_section_id: nanopore
+  tool_panel_section_label: Nanopore
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: xpore
   owner: artbio
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: minimap2
-  owner: iuc
+- name: tarfast5
+  owner: artbio
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -1889,11 +1889,6 @@ tools:
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: tarfast5
-  owner: artbio
-  tool_panel_section_id: nanopore
-  tool_panel_section_label: Nanopore
-  tool_shed_url: testtoolshed.g2.bx.psu.edu
 - name: pangolin
   owner: iuc
   tool_panel_section_id: covid-19
@@ -1904,11 +1899,6 @@ tools:
   tool_panel_section_id: covid-19
   tool_panel_section_label: Covid-19
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: nextclade
-  owner: iuc
-  tool_panel_section_id: covid-19
-  tool_panel_section_label: Covid-19
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: ivar_trim
   owner: iuc
   tool_panel_section_id: covid-19
@@ -1969,6 +1959,21 @@ tools:
   tool_panel_section_id: flux_cytometry
   tool_panel_section_label: Flux Cytometry
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: beagle
+  owner: iuc
+  tool_panel_section_id: human_genetics
+  tool_panel_section_label: HUMAN GENETICS
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: beagle4_0
+  owner: bobbledavidson
+  tool_panel_section_id: human_genetics
+  tool_panel_section_label: HUMAN GENETICS
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: justdiff
+  owner: artbio
+  tool_panel_section_id: text
+  tool_panel_section_label: text
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: data_manager_bowtie_index_builder
   owner: iuc
   tool_panel_section_id: None
@@ -2009,12 +2014,27 @@ tools:
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: data_manager_kallisto_index_builder
+  owner: iuc
+  tool_panel_section_id: None
+  tool_panel_section_label: None
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: data_manager_star_index_builder
   owner: iuc
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_kallisto_index_builder
+- name: data_manager_vep_cache_downloader
+  owner: iuc
+  tool_panel_section_id: None
+  tool_panel_section_label: None
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: data_manager_snpeff
+  owner: iuc
+  tool_panel_section_id: None
+  tool_panel_section_label: None
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: data_manager_snpsift_dbnsfp
   owner: iuc
   tool_panel_section_id: None
   tool_panel_section_label: None
diff --git a/environments/ARTbio/files/galaxy/config/job_conf.xml b/environments/ARTbio/files/galaxy/config/job_conf.xml
deleted file mode 100644
index d5f1c16..0000000
--- a/environments/ARTbio/files/galaxy/config/job_conf.xml
+++ /dev/null
@@ -1,158 +0,0 @@
-<job_conf>
-    <plugins workers="8">
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
-        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
-            <param id="drmaa_library_path">/usr/lib/slurm-drmaa/lib/libdrmaa.so</param>
-        </plugin>
-    </plugins>
-
-    <handlers assign_with="db-skip-locked" default="handlers">
-        <handler id="handler_0" tags="handlers"/>
-        <handler id="handler_1" tags="handlers"/>
-        <handler id="handler_2" tags="handlers"/>
-        <handler id="handler_3" tags="handlers"/>
-    </handlers>
-
-    <destinations default="single">
-        <destination id="local" runner="local"/>
-        <destination id="gce_multicore" runner="local">
-            <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
-        </destination>
-        <destination id="single" runner="slurm">
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-           <param id="nativeSpecification">--partition=debug --ntasks=1</param>
-        </destination>
-        <destination id="double" runner="slurm">
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-           <param id="nativeSpecification">--partition=debug --ntasks=2</param>
-        </destination>
-        <destination id="cluster_4" runner="slurm">
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-           <param id="nativeSpecification">--partition=debug --ntasks=4</param>
-        </destination>
-        <destination id="cluster" runner="slurm">
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-           <param id="nativeSpecification">--partition=debug --ntasks=8</param>
-        </destination>
-        <destination id="cluster_heavy" runner="slurm">
-           <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="nativeSpecification">--partition=debug --ntasks=16</param>
-        </destination>
-        <destination id="cluster_superheavy" runner="slurm">
-           <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="nativeSpecification">--partition=debug --ntasks=64</param>
-        </destination>
-        <destination id="samtools_fastx" runner="slurm">
-           <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="nativeSpecification">--partition=debug --ntasks=5</param>
-        </destination>
-        <destination id="lumpy_smoove" runner="slurm">
-           <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="nativeSpecification">--partition=debug --ntasks=32</param>
-        </destination>
-        <destination id="java_cluster" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <env id="_JAVA_OPTIONS">-Xmx40g</env>
-            <env id="_JAVA_OPTIONS">-Xms512m</env>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=4 --share</param>
-        </destination>
-    </destinations>
-    <limits>
-        <limit type="destination_total_concurrent_jobs" id="lumpy_smoove">32</limit>
-        <limit type="destination_total_concurrent_jobs" id="cluster">8</limit>
-        <limit type="destination_total_concurrent_jobs" id="cluster_4">20</limit>
-        <limit type="destination_total_concurrent_jobs" id="cluster_heavy">4</limit>
-        <limit type="destination_total_concurrent_jobs" id="cluster_superheavy">1</limit>
-        <limit type="destination_total_concurrent_jobs" id="single">60</limit>
-        <limit type="destination_total_concurrent_jobs" id="double">30</limit>
-        <limit type="destination_total_concurrent_jobs" id="samtools_fastx">30</limit>
-        <limit type="destination_user_concurrent_jobs" id="java_cluster">4</limit>
-
-
-        <limit type="anonymous_user_concurrent_jobs">1</limit>
-
-        <limit type="destination_user_concurrent_jobs" id="lumpy_smoove">32</limit>
-        <limit type="destination_user_concurrent_jobs" id="cluster">8</limit>
-        <limit type="destination_user_concurrent_jobs" id="cluster_4">20</limit>
-        <limit type="destination_user_concurrent_jobs" id="cluster_heavy">6</limit>
-        <limit type="destination_user_concurrent_jobs" id="cluster_superheavy">1</limit>
-        <limit type="destination_user_concurrent_jobs" id="single">60</limit>
-        <limit type="destination_user_concurrent_jobs" id="double">30</limit>
-        <limit type="destination_user_concurrent_jobs" id="samtools_fastx">30</limit>
-        <limit type="destination_user_concurrent_jobs" id="java_cluster">4</limit>
-    </limits>
-   <tools>
-        <tool id="bcftools_annotate" destination="cluster" />
-        <tool id="bcftools_norm" destination="cluster" />
-        <tool id="bowtie" destination="cluster_heavy"/>
-        <tool id="bowtie2" destination="cluster_heavy"/>
-        <tool id="bowtieForSmallRNA" destination="cluster_heavy"/>
-        <tool id="bowtie_wrapper" destination="cluster_heavy"/>
-        <tool id="bwa" destination="cluster_heavy"/>
-        <tool id="bwa_mem" destination="cluster_heavy"/>
-        <tool id="bwa_wrappers" destination="cluster_heavy"/>
-        <tool id="cuffdiff" destination="cluster_heavy"/>
-        <tool id="cutadapt" destination="cluster_heavy" />
-        <tool id="deeptools_multi_bam_summary" destination="cluster_heavy"/>
-        <tool id="deeptools_plot_correlation" destination="cluster_heavy"/>
-        <tool id="deeptools_compute_matrix" destination="cluster_heavy"/>
-        <tool id="deeptools_bam_coverage" destination="cluster_heavy"/>
-        <tool id="deeptools_plot_coverage" destination="cluster"/>
-        <tool id="deeptools_plot_fingerprint" destination="cluster_heavy"/>
-        <tool id="dexseq_count" destination="double"/>
-        <tool id="dexseq" destination="double"/>
-        <tool id="fastq_dump" destination="double" />
-        <tool id="freebayes" destination="cluster" />
-        <tool id="featurecounts" destination="cluster_4" />
-        <tool id="Group" destination="single" />
-        <tool id="guppy-basecaller" destination="cluster"/>
-        <tool id="hisat2" destination="cluster_heavy"/>
-        <tool id="hisat2_index_builder_data_manager" destination="cluster_4"/>
-        <tool id="lumpy_smoove" destination="lumpy_smoove" />
-        <tool id="lumpy_sv" destination="cluster"/>
-        <tool id="macs2_callpeak" destination="cluster_heavy"/>
-        <tool id="manta" destination="cluster"/>
-        <tool id="minimap2" destination="cluster"/>
-        <tool id="mircounts" destination="cluster"/>
-        <tool id="nanopolish_eventalign" destination="cluster_heavy"/>
-        <tool id="ncbi_blastx_wrapper" destination="cluster_heavy"/>
-        <tool id="ncbi_blastn_wrapper" destination="cluster_heavy"/>
-        <tool id="ncbi_blastp_wrapper" destination="cluster_heavy"/>
-        <tool id="ngsplot" destination="cluster"/>
-        <tool id="picard_SamToFastq" destination="single" />
-        <tool id="repenrich" destination="cluster_heavy"/>
-        <tool id="rna_star" destination="cluster"/>
-        <tool id="rna_star_index_builder_data_manager" destination="cluster"/>
-        <tool id="rna_starsolo" destination="cluster"/>
-        <tool id="rsembowtie" destination="cluster"/>
-        <tool id="rsembowtie2" destination="cluster_heavy"/>
-        <tool id="samtools_cram_to_bam" destination="cluster"/>
-        <tool id="samtools_slice_bam" destination="cluster"/>
-        <tool id="samtools_view" destination="cluster"/>
-        <tool id="samtools_rmdup" destination="cluster"/>
-        <tool id="samtools_fastx" destination="cluster_4"/>
-        <tool id="samtool_filter2" destination="cluster_4"/>
-        <tool id="small_rna_maps" destination="double"/>
-        <tool id="snpSift_annotate" destination="java_cluster"/>
-        <tool id="snpSift_filter" destination="java_cluster"/>
-        <tool id="snpEff" destination="java_cluster"/>
-        <tool id="sr_bowtie_dataset_annotation" destination="cluster_heavy"/>
-        <tool id="tarfast5" destination="cluster"/>
-        <tool id="table_annovar" destination="cluster"/>
-        <tool id="tp_grep_tool" destination="single" />
-        <tool id="tophat2" destination="cluster_heavy"/>
-        <tool id="vsearch_clustering" destination="cluster_superheavy"/>
-        <tool id="xpore_dataprep" destination="cluster_heavy"/>
-        <tool id="xpore_diffmod" destination="cluster_heavy"/>
-        <tool id="sambamba_sample_or_filter" destination="cluster"/>
-    </tools>
-</job_conf>
diff --git a/environments/ARTbio/files/galaxy/config/job_conf.yml b/environments/ARTbio/files/galaxy/config/job_conf.yml
new file mode 100644
index 0000000..24b26a8
--- /dev/null
+++ b/environments/ARTbio/files/galaxy/config/job_conf.yml
@@ -0,0 +1,301 @@
+# This file is managed by Ansible.
+# Do not edit this file manually. Any changes will be automatically reverted.
+
+runners:
+  local_runner:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 8
+  slurm:
+    load: galaxy.jobs.runners.slurm:SlurmJobRunner
+    drmaa_library_path: /usr/lib/slurm-drmaa/lib/libdrmaa.so
+
+handling:
+  assign:
+    - db-skip-locked
+  processes:
+    handler0:
+    handler1:
+    handler2:
+    handler3:
+
+# artbio has 72 CPUs
+execution:
+  default: cluster_1
+  environments:
+    local_env:
+      runner: local_runner
+      tmp_dir: true
+    gce_multicore:
+      runner: local_runner
+      local_slots: 2
+      embed_metadata_in_job: true
+    cluster_1:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=1"
+    cluster_2:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=2"
+    cluster_4:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=4"
+    cluster_8:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=8"
+    cluster_16:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=16"
+    cluster_64:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=64"
+    samtools_fastx:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=5"
+    java_cluster:
+      runner: slurm # if not working, try drmaa runner
+      nativeSpecification: "--partition=debug --ntasks=1"
+      env:
+        - name: '_JAVA_OPTIONS'
+          value: '-Xmx40g -Xms512m'
+        - file: '/home/galaxy/galaxy/.venv/bin/activate'
+
+limits:
+  - type: anonymous_user_concurrent_jobs
+    value: 1
+  - type: registered_user_concurrent_jobs
+    value: 64
+
+  - type: environment_total_concurrent_jobs
+    id: cluster_1
+    value: 60
+  - type: environment_total_concurrent_jobs
+    id: cluster_2
+    value: 30
+  - type: environment_total_concurrent_jobs
+    id: cluster_4
+    value: 15
+  - type: environment_total_concurrent_jobs
+    id: cluster_8
+    value: 8
+  - type: environment_total_concurrent_jobs
+    id: cluster_16
+    value: 4
+  - type: environment_total_concurrent_jobs
+    id: java_cluster
+    value: 32
+  - type: environment_total_concurrent_jobs
+    id: samtools_fastx
+    value: 30
+
+tools:
+  - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
+    environment: local_env
+
+  - id: "artbio_bam_cleaning"
+    destination: "cluster_8"
+
+  - id: "bcftools_annotate"
+    destination: "cluster_8" 
+
+  - id: "bcftools_mpileup"
+    destination: "cluster_8" 
+
+  - id: "bcftools_norm"
+    destination: "cluster_1" 
+
+  - id: "bowtie_wrapper"
+    destination: "cluster_16"
+
+  - id: "bowtie"
+    destination: "cluster_16"
+
+  - id: "bowtie2"
+    destination: "cluster_16"
+
+  - id: "bowtieForSmallRNA"
+    destination: "cluster_16"
+
+  - id: "bwa_mem"
+    destination: "cluster_16"
+
+  - id: "bwa_wrappers"
+    destination: "cluster_16"
+
+  - id: "bwa"
+    destination: "cluster_16"
+
+  - id: "cuffdiff"
+    destination: "cluster_16"
+
+  - id: "cutadapt"
+    destination: "cluster_16" 
+
+  - id: "deeptools_bam_compare"
+    destination: "cluster_16"
+
+  - id: "deeptools_bam_coverage"
+    destination: "cluster_16"
+
+  - id: "deeptools_compute_matrix"
+    destination: "cluster_16"
+
+  - id: "deeptools_multi_bam_summary"
+    destination: "cluster_16"
+
+  - id: "deeptools_plot_correlation"
+    destination: "cluster_16"
+
+  - id: "deeptools_plot_coverage"
+    destination: "cluster_8"
+
+  - id: "deeptools_plot_fingerprint"
+    destination: "cluster_16"
+
+  - id: "dexseq_count"
+    destination: "cluster_2"
+
+  - id: "dexseq"
+    destination: "cluster_2"
+
+  - id: "fastqc"
+    destination: "java_cluster"
+
+  - id: "fastq_dump"
+    destination: "cluster_2" 
+
+  - id: "featurecounts"
+    destination: "cluster_4" 
+
+  - id: "freebayes"
+    destination: "cluster_1" 
+
+  - id: "Group"
+    destination: "cluster_1" 
+
+  - id: "guppy-basecaller"
+    destination: "cluster_8"
+
+  - id: "hisat2_index_builder_data_manager"
+    destination: "cluster_4"
+
+  - id: "hisat2"
+    destination: "cluster_16"
+
+  - id: "justgzip"
+    destination: "cluster_8" 
+
+  - id: "kallisto_quant"
+    destination: "cluster_8"
+
+  - id: "lumpy_smoove"
+    destination: "lumpy_smoove" 
+
+  - id: "lumpy_sv"
+    destination: "cluster_8"
+
+  - id: "macs2_callpeak"
+    destination: "cluster_16"
+
+  - id: "manta"
+    destination: "cluster_8"
+
+  - id: "minimap2"
+    destination: "cluster_8"
+
+  - id: "mircounts"
+    destination: "cluster_8"
+
+  - id: "nanopolish_eventalign"
+    destination: "cluster_16"
+
+  - id: "ncbi_blastn_wrapper"
+    destination: "cluster_16"
+
+  - id: "ncbi_blastp_wrapper"
+    destination: "cluster_16"
+
+  - id: "ncbi_blastx_wrapper"
+    destination: "cluster_16"
+
+  - id: "ngsplot"
+    destination: "cluster_8"
+
+  - id: "picard_FilterSamReads"
+    destination: "java_cluster" 
+
+  - id: "picard_SamToFastq"
+    destination: "cluster_1" 
+
+  - id: "repenrich"
+    destination: "cluster_16"
+
+  - id: "rna_star_index_builder_data_manager"
+    destination: "cluster_8"
+
+  - id: "rna_star"
+    destination: "cluster_8"
+
+  - id: "rna_starsolo"
+    destination: "cluster_8"
+
+  - id: "rsembowtie"
+    destination: "cluster_8"
+
+  - id: "rsembowtie2"
+    destination: "cluster_16"
+
+  - id: "sambamba_sample_or_filter"
+    destination: "cluster_8"
+
+  - id: "samtool_filter2"
+    destination: "cluster_4"
+
+  - id: "samtools_cram_to_bam"
+    destination: "cluster_8"
+
+  - id: "samtools_fastx"
+    destination: "samtools_fastx"
+
+  - id: "samtools_rmdup"
+    destination: "cluster_8"
+
+  - id: "samtools_slice_bam"
+    destination: "cluster_8"
+
+  - id: "samtools_view"
+    destination: "cluster_8"
+
+  - id: "small_rna_maps"
+    destination: "cluster_2"
+
+  - id: "snpEff"
+    destination: "java_cluster"
+
+  - id: "snpSift_annotate"
+    destination: "java_cluster"
+
+  - id: "snpSift_filter"
+    destination: "java_cluster"
+
+  - id: "sr_bowtie_dataset_annotation"
+    destination: "cluster_16"
+
+  - id: "table_annovar"
+    destination: "cluster_8"
+
+  - id: "tarfast5"
+    destination: "cluster_8"
+
+  - id: "tophat2"
+    destination: "cluster_16"
+
+  - id: "tp_grep_tool"
+    destination: "cluster_1" 
+
+  - id: "vsearch_clustering"
+    destination: "cluster_64"
+
+  - id: "xpore_dataprep"
+    destination: "cluster_16"
+
+  - id: "xpore_diffmod"
+    destination: "cluster_16"
diff --git a/environments/ARTbio/files/galaxy/html/welcome.html b/environments/ARTbio/files/galaxy/html/welcome.html
index bd788db..e4699e8 100644
--- a/environments/ARTbio/files/galaxy/html/welcome.html
+++ b/environments/ARTbio/files/galaxy/html/welcome.html
@@ -31,18 +31,18 @@
         <!-- -->
         <div class="alert alert-success" style="margin-top: 0.5em">
             <div>
-                <h4><p>
-                The error reporting using automated emails has been fixed.
-                You can report your mistakes and encountered bugs again!
-                </p>
-                <p>For better resilience to troubles, the deployment of the Galaxy server dedicated to our users is
+                <h4>
+                <p>
+                    For better resilience to troubles, the deployment of the Galaxy server dedicated to our users is
                     automated using the <a href="/ARTbio/galaxyXpand" target="_blank">galaxyXpand</a>
-                Ansible playbook.
+                    Ansible playbook.
+                </p>
+                <p>
+                    Users owning an account on this server may request tool installations by raising
+                    a pull request after editing the <a href="/ARTbio/galaxyXpand/blob/main/environments/ARTbio/files/galaxy/config/artbio_tool_list.yml" target="_blank">
+                    artbio_tool_list.yml </a> on our <a href="/ARTbio/galaxyXpand" target="_blank"> GitHub galaxyXpand </a> repository.
                 </p>
-                <p>Users owning an account on this server may request tool installations by raising
-                   a pull request after editing the <a href="/ARTbio/galaxyXpand/blob/main/environments/ARTbio/files/galaxy/config/artbio_tool_list.yml" target="_blank">
-                artbio_tool_list.yml </a> on our <a href="/ARTbio/galaxyXpand" target="_blank"> GitHub galaxyXpand </a> repository.
-                </p></h4>
+                </h4>
             </div>
         </div>
         <!-- -->
diff --git a/environments/ARTbio/group_vars/all/galaxy b/environments/ARTbio/group_vars/all/galaxy
index f260dac..ae406ce 100644
--- a/environments/ARTbio/group_vars/all/galaxy
+++ b/environments/ARTbio/group_vars/all/galaxy
@@ -1,28 +1,29 @@
 ---
-# overwrite properly the previous uwgi-based galaxykickstart (default: no)
-
 # Galaxy
 galaxy_additional_venv_packages: drmaa
+galaxy_commit_id: release_23.0
+galaxy_config_dir: "{{ galaxy_server_dir }}/config"
+galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
 galaxy_create_user: true
-galaxy_separate_privileges: true
-galaxy_privsep_user: "{{ galaxy_user }}"
+galaxy_force_checkout: true
 galaxy_layout: legacy
-galaxy_server_dir: "{{ galaxy_root }}/galaxy"
-galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
+galaxy_manage_cleanup: yes  # Install a cron job to clean up Galaxy framework and job execution temporary
 galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
-galaxy_config_dir: "{{ galaxy_server_dir }}/config"
-galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
+galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
+galaxy_privsep_user: "{{ galaxy_user }}"
 galaxy_root: /home/galaxy
-galaxy_user: {name: galaxy, shell: /bin/bash}
-galaxy_commit_id: release_22.05
-galaxy_force_checkout: true
+galaxy_separate_privileges: true
+galaxy_server_dir: "{{ galaxy_root }}/galaxy"
 galaxy_tool_dependency_dir: "{{ galaxy_root }}/tool_dependencies"
-galaxy_manage_cleanup: yes  # Install a cron job to clean up Galaxy framework and job execution temporary
+galaxy_user: {name: galaxy, shell: /bin/bash}
+miniconda_channels: ['conda-forge', 'bioconda', 'defaults']
 miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
-miniconda_version: 4.7.12
-miniconda_manage_dependencies: false
+miniconda_version: 23.11
+
 galaxy_config:
   galaxy:
+    brand: "🧬 ARTbio Users"
+    builds_file_path: shared/ucsc/builds.txt
     admin_users: !vault |
           $ANSIBLE_VAULT;1.1;AES256
           63643139343762383638653130303436363532333730326339373338303464303132646164636361
@@ -32,27 +33,21 @@ galaxy_config:
           64616530643039326363393338336464633635623631303634356265373735386138356134636439
           66386235666133626339666233646138613932336335646664316163616534663330306634306138
           393839386231643763643165376530623464
-    allow_library_path_paste: true
-    allow_user_dataset_purge: true
-    allow_user_deletion: true
-    allow_user_impersonation: true
-    brand: "🧬 ARTbio Users"
-    builds_file_path: shared/ucsc/builds.txt
-    container_resolvers_config_file: ''
-    data_dir: /home/galaxy/galaxy/database
-    data_manager_config_file: /home/galaxy/galaxy/config/data_manager_conf.xml.sample
-    database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
-    datatypes_config_file: /home/galaxy/galaxy/config/datatypes_conf.xml.sample
-    dependency_resolvers_config_file: /home/galaxy/galaxy/config/dependency_resolvers_conf.xml
     display_servers: hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
-    email_from: !vault |
+    smtp_username: !vault |
           $ANSIBLE_VAULT;1.1;AES256
-          30663537623338346331663166663830386230386136356361346231626463383064363166336663
-          6464363832346330643136623961326438653266386431390a656438323963356636613835653162
-          39363266376262343236353535393435613332356262383130653838386261383866366636313230
-          3463376437376438320a383863333966383038343539363764396365333431336533633065623934
-          30386362636230323035613263336535333161633835633439346662326339633665
-    enable_quotas: true
+          35363239623130313538386637313462376235386364363466663631623931636666613166653165
+          3433346435643565313035633738353430633036333761340a393539623838666564303462363539
+          39333033383264306437326266646664356134313666643736366261306230643936383263383535
+          6161346134376632340a616330313936353566613332633833326337623132386639626631633830
+          30323130323632646264326466373337396230393131353832646536326135653633
+    smtp_password: !vault |
+          $ANSIBLE_VAULT;1.1;AES256
+          63663039356536353639356432326533646539376165626162376162643938626531623434643263
+          3432356132303430356139353332393537326361626536310a346264313136343663623566303234
+          61666234323161623863306431656239653836323934303866363739623735393332613861643531
+          3532663561316632350a613563376434363466623032373561383062366264636333393937333139
+          31326538393739656335313630616234626430373331636330313663316638373863
     error_email_to: !vault |
           $ANSIBLE_VAULT;1.1;AES256
           65306633343037366561326632393730393731363066336566316430346638326630353632623638
@@ -60,12 +55,17 @@ galaxy_config:
           38383762643363383039353732623434636631626135613733636130393634303932653136656230
           6361623730303935660a666461396562396666666466633765616633643338353931613035336330
           32333532396466653665346135346462653239616234646639666462316137613565
-    expose_dataset_path: true
-    expose_potentially_sensitive_job_metrics: true
-    external_service_type_config_file: /home/galaxy/galaxy/config/external_service_types_conf.xml.sample
+    email_from: !vault |
+          $ANSIBLE_VAULT;1.1;AES256
+          30663537623338346331663166663830386230386136356361346231626463383064363166336663
+          6464363832346330643136623961326438653266386431390a656438323963356636613835653162
+          39363266376262343236353535393435613332356262383130653838386261383866366636313230
+          3463376437376438320a383863333966383038343539363764396365333431336533633065623934
+          30386362636230323035613263336535333161633835633439346662326339633665
+    smtp_server: 'smtp.gmail.com:587'
+    database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
     file_path: datasets
-    ftp_upload_dir: /home/galaxy/galaxy/database/ftp
-    ftp_upload_site: ftp://134.157.185.153
+    object_store_store_by: id
     id_secret: !vault |
           $ANSIBLE_VAULT;1.1;AES256
           61363538613537363565396330346437636632396632326434663963393532336265626163323933
@@ -74,47 +74,47 @@ galaxy_config:
           3865316261666665310a343638393663616336343233393863633065303031656264663063636635
           33633238313161636239633532376563393261386439663762653566613339616261376366303731
           6264376664373139646366656434303766353836353436613439
-    integrated_tool_panel_config: /home/galaxy/galaxy/config/integrated_tool_panel.xml
-    job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
-    job_metrics_config_file: /home/galaxy/galaxy/config/job_metrics_conf.xml
-    job_working_directory: /home/galaxy/galaxy/database/jobs
-    len_file_path: /home/galaxy/galaxy/config/len
-    migrated_tools_config: /home/galaxy/galaxy/config/migrated_tools_conf.xml
+    check_migrate_tools: false
+    tool_data_path: "{{ galaxy_server_dir }}/tool-data"
+    job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
+    allow_library_path_paste: true
+    watch_tool_data_dir: true
+    # File serving perfomance
     nginx_x_accel_redirect_base: /_x_accel_redirect
-    object_store_store_by: id
-    openid_config_file: /home/galaxy/galaxy/config/openid_conf.xml.sample
+    # SQL Performance
+    slow_query_log_threshold: 5
+    enable_per_request_sql_debugging: true
+    # Automation / Ease of Use / User-facing features
+    allow_user_dataset_purge: true
+    enable_quotas: true
+    allow_user_deletion: true
+    allow_user_impersonation: true
+    watch_job_rules: 'auto'
+    allow_path_paste: true
+    expose_user_name: true
+    expose_dataset_path: true
+    expose_potentially_sensitive_job_metrics: true
     require_login: true
-    shed_data_manager_config_file: /home/galaxy/galaxy/config/shed_data_manager_conf.xml
-    shed_tool_config_file: /home/galaxy/galaxy/config/shed_tool_conf.xml
-    shed_tool_data_table_config: /home/galaxy/galaxy/config/shed_tool_data_table_conf.xml
-    smtp_password: !vault |
-          $ANSIBLE_VAULT;1.1;AES256
-          63663039356536353639356432326533646539376165626162376162643938626531623434643263
-          3432356132303430356139353332393537326361626536310a346264313136343663623566303234
-          61666234323161623863306431656239653836323934303866363739623735393332613861643531
-          3532663561316632350a613563376434363466623032373561383062366264636333393937333139
-          31326538393739656335313630616234626430373331636330313663316638373863
-    smtp_server: 'smtp.gmail.com:587'
-    smtp_username: !vault |
-          $ANSIBLE_VAULT;1.1;AES256
-          35363239623130313538386637313462376235386364363466663631623931636666613166653165
-          3433346435643565313035633738353430633036333761340a393539623838666564303462363539
-          39333033383264306437326266646664356134313666643736366261306230643936383263383535
-          6161346134376632340a616330313936353566613332633833326337623132386639626631633830
-          30323130323632646264326466373337396230393131353832646536326135653633
+    # Debugging
+    cleanup_job: onsuccess
+    # Tool security
+    outputs_to_working_directory: true
+    new_user_dataset_access_role_default_private: true # Make datasets private by default
+    # Miscellaneous
+    ftp_upload_dir: /home/galaxy/galaxy/database/ftp
+    ftp_upload_site: ftp://134.157.185.153
+    integrated_tool_panel_config: /home/galaxy/galaxy/config/integrated_tool_panel.xml
+    len_file_path: /home/galaxy/galaxy/config/len
     static_enabled: false
-    tool_config_file: /home/galaxy/galaxy/config/tool_conf.xml
-    tool_data_path: "{{ galaxy_server_dir }}/tool-data"
+    tool_config_file: /home/galaxy/galaxy/config/tool_conf.xml.sample
     tool_data_table_config_path: /home/galaxy/galaxy/config/tool_data_table_conf.xml.sample
-    tool_dependency_dir: /home/galaxy/tool_dependencies
     tool_sheds_config_file: /home/galaxy/galaxy/config/tool_sheds_conf.xml
-    ucsc_build_sites: /home/galaxy/galaxy/tool-data/shared/ucsc/ucsc_build_sites.txt.sample
-    visualization_plugins_directory: config/plugins/visualizations
-    watch_tool_data_dir: true
 
   gravity:
+    process_manager: systemd
     galaxy_root: "{{ galaxy_server_dir }}"
-    app_server: gunicorn
+    galaxy_user: "{{ galaxy_user_name }}"
+    virtualenv: "{{ galaxy_venv_dir }}"
     gunicorn:
       # listening options
       bind: "unix:{{ galaxy_config_dir }}/gunicorn.sock"
@@ -135,7 +135,7 @@ galaxy_config:
 
 # deploy galaxy configuration files
 galaxy_config_files:
-  - src: environments/ARTbio/files/galaxy/config/job_conf.xml
+  - src: environments/ARTbio/files/galaxy/config/job_conf.yml
     dest: "{{ galaxy_config.galaxy.job_config_file }}"
   - src: environments/ARTbio/files/galaxy/config/tool_conf.xml
     dest: "{{ galaxy_config_dir }}/tool_conf.xml"
diff --git a/environments/ARTbio/group_vars/all/nginx b/environments/ARTbio/group_vars/all/nginx
index 8aec0b3..6c70457 100644
--- a/environments/ARTbio/group_vars/all/nginx
+++ b/environments/ARTbio/group_vars/all/nginx
@@ -1,6 +1,7 @@
 ---
 # NGINX
 nginx_server_src_dir: environments/ARTbio/templates/nginx/
+nginx_selinux_allow_local_connections: true
 nginx_ssl_servers:
   - galaxy
 nginx_enable_default_server: false
diff --git a/environments/ARTbio/group_vars/all/slurm b/environments/ARTbio/group_vars/all/slurm
index fa99095..406f6dd 100644
--- a/environments/ARTbio/group_vars/all/slurm
+++ b/environments/ARTbio/group_vars/all/slurm
@@ -11,3 +11,14 @@ slurm_config:
   SelectType: select/cons_res
   SelectTypeParameters: CR_Core_Memory
 
+slurm_nodes:
+  - name: "localhost"
+    CPUs: 72
+    RealMemory: 773938
+
+slurm_partitions:
+  - name: debug
+    Default: YES
+    DefMemPerCPU: 10749
+    Nodes: "localhost"
+
diff --git a/environments/ARTbio/group_vars/dbservers.yml b/environments/ARTbio/group_vars/dbservers.yml
new file mode 120000
index 0000000..2ef78cc
--- /dev/null
+++ b/environments/ARTbio/group_vars/dbservers.yml
@@ -0,0 +1 @@
+../../dbservers.yml
\ No newline at end of file
diff --git a/environments/ARTbio/hosts b/environments/ARTbio/hosts
index 3e18fb5..c4d8184 100644
--- a/environments/ARTbio/hosts
+++ b/environments/ARTbio/hosts
@@ -1,3 +1,5 @@
-[Conect]
-
+[ARTbio]
 localhost  ansible_connection=local ansible_user=root
+
+[dbservers:children]
+ARTbio
diff --git a/environments/ARTbio/templates/nginx/galaxy.j2 b/environments/ARTbio/templates/nginx/galaxy.j2
index bfb9c71..3e241c9 100644
--- a/environments/ARTbio/templates/nginx/galaxy.j2
+++ b/environments/ARTbio/templates/nginx/galaxy.j2
@@ -17,6 +17,10 @@ server {
     # The virtualhost is our domain name
     server_name   "{{ inventory_hostname }}";
 
+    proxy_read_timeout 300;
+    proxy_connect_timeout 300;
+    proxy_send_timeout 300; 
+
     # Our log files will go here.
     access_log /var/log/nginx/access.log;
     error_log /var/log/nginx/error.log;
diff --git a/environments/Conect/files/galaxy/config/conect_tool_list.yml b/environments/Conect/files/galaxy/config/conect_tool_list.yml
index 9b7efcd..01732af 100644
--- a/environments/Conect/files/galaxy/config/conect_tool_list.yml
+++ b/environments/Conect/files/galaxy/config/conect_tool_list.yml
@@ -9,57 +9,42 @@ tools:
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: small_rna_signatures
-  owner: artbio
-  tool_panel_section_id: artbio_tools
-  tool_panel_section_label: ARTbio tools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sigmut
-  owner: artbio
-  tool_panel_section_id: artbio_tools
-  tool_panel_section_label: ARTbio tools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: pathifier
-  owner: bellenger-l
-  tool_panel_section_id: artbio_tools
-  tool_panel_section_label: ARTbio tools
-  tool_shed_url: testtoolshed.g2.bx.psu.edu
-- name: gsc_mannwhitney_de
+- name: small_rna_maps
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_filter_genes
+- name: probecoverage
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gsc_high_dimensions_visualisation
+- name: mircounts
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bamparse
+- name: justgzip
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bigwig_to_wig
+- name: justdiff
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blast_unmatched
+- name: gsc_mannwhitney_de
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blastx_to_scaffold
+- name: gsc_high_dimensions_visualisation
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: cpm_tpm_rpk
+- name: gsc_filter_genes
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
@@ -69,67 +54,47 @@ tools:
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fishertest
-  owner: artbio
-  tool_panel_section_id: artbio_tools
-  tool_panel_section_label: ARTbio tools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: justdiff
+- name: cherry_pick_fasta
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: justgzip
+- name: bamparse
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: mircounts
+- name: sigmut
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: probecoverage
-  owner: artbio
+- name: pathifier
+  owner: bellenger-l
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
-  tool_shed_url: toolshed.g2.bx.psu.edu
+  tool_shed_url: testtoolshed.g2.bx.psu.edu
 - name: repenrich
   owner: artbio
   tool_panel_section_id: artbio_tools
   tool_panel_section_label: ARTbio tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: small_rna_maps
-  owner: artbio
-  tool_panel_section_id: artbio_tools
-  tool_panel_section_label: ARTbio tools
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: rsem
-  owner: artbio
-  tool_panel_section_id: aligners
-  tool_panel_section_label: Aligners
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: varscan_version_2
   owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: circos
-  owner: iuc
-  tool_panel_section_id: plots
-  tool_panel_section_label: Graph/Display Data
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: rgrnastar
   owner: iuc
   tool_panel_section_id: aligners
   tool_panel_section_label: Aligners
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bwa_mem2
+- name: hisat2
   owner: iuc
   tool_panel_section_id: aligners
   tool_panel_section_label: Aligners
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bbtools_bbmap
+- name: bwa_mem2
   owner: iuc
   tool_panel_section_id: aligners
   tool_panel_section_label: Aligners
@@ -139,23 +104,23 @@ tools:
   tool_panel_section_id: aligners
   tool_panel_section_label: Aligners
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bowtie2
-  owner: devteam
+- name: bbtools_bbmap
+  owner: iuc
   tool_panel_section_id: aligners
   tool_panel_section_label: Aligners
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: hisat2
-  owner: iuc
+- name: bowtie2
+  owner: devteam
   tool_panel_section_id: aligners
   tool_panel_section_label: Aligners
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_reheader
-  owner: devteam
+- name: samtools_view
+  owner: iuc
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_view
-  owner: iuc
+- name: samtools_stats
+  owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -164,107 +129,107 @@ tools:
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_markdup
-  owner: iuc
+- name: samtools_sort
+  owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtool_filter2
+- name: samtools_slice_bam
   owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_bedcov
+- name: samtools_reheader
   owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_merge
-  owner: iuc
+- name: samtools_phase
+  owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_calmd
+- name: samtools_mpileup
   owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bam_to_sam
-  owner: devteam
+- name: samtools_merge
+  owner: iuc
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_rmdup
-  owner: devteam
+- name: samtools_markdup
+  owner: iuc
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_sort
+- name: samtools_idxstats
   owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_slice_bam
-  owner: devteam
+- name: samtools_fixmate
+  owner: iuc
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_idxstats
-  owner: devteam
+- name: samtools_fastx
+  owner: iuc
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sam_to_bam
-  owner: devteam
+- name: samtools_depth
+  owner: iuc
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_flagstat
+- name: samtools_calmd
   owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_stats
+- name: samtools_bedcov
   owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_mpileup
+- name: sam_to_bam
   owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: rmarkdown_samtools_flagstat
-  owner: mingchen0919
+- name: bam_to_sam
+  owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_depth
-  owner: iuc
+- name: samtool_filter2
+  owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_fastx
-  owner: iuc
+- name: samtools_rmdup
+  owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_fixmate
-  owner: iuc
+- name: samtools_flagstat
+  owner: devteam
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_phase
-  owner: devteam
+- name: rmarkdown_samtools_flagstat
+  owner: mingchen0919
   tool_panel_section_id: samtools
   tool_panel_section_label: SAMtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bedtools
+- name: crossmap_bed
   owner: iuc
   tool_panel_section_id: bedtools
   tool_panel_section_label: BEDtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: crossmap_bed
+- name: bedtools
   owner: iuc
   tool_panel_section_id: bedtools
   tool_panel_section_label: BEDtools
@@ -274,82 +239,72 @@ tools:
   tool_panel_section_id: picardtools
   tool_panel_section_label: PICARD tools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: cutadapt
-  owner: lparsons
-  tool_panel_section_id: ngs:_qc_and_manipulation
-  tool_panel_section_label: 'NGS: QC and manipulation'
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: artbio_bam_cleaning
-  owner: artbio
+- name: trimmomatic
+  owner: pjbriggs
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: khmer_normalize_by_median
+- name: seqtk
   owner: iuc
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fastx_trimmer
-  owner: devteam
+- name: multiqc
+  owner: iuc
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: multiqc
+- name: khmer_normalize_by_median
   owner: iuc
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fastqc
+- name: fastx_trimmer
   owner: devteam
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: trimmomatic
-  owner: pjbriggs
+- name: fastx_reverse_complement
+  owner: devteam
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fastq_paired_end_deinterlacer
-  owner: devteam
+- name: cutadapt
+  owner: lparsons
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: rseqc
-  owner: nilesh
+- name: artbio_bam_cleaning
+  owner: artbio
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fastx_reverse_complement
+- name: fastqc
   owner: devteam
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: seqtk
-  owner: iuc
+- name: fastq_paired_end_deinterlacer
+  owner: devteam
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcftools_isec
+- name: vcffilter
   owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcffixup
+- name: vcf2tsv
   owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: snpsift_dbnsfp
-  owner: iuc
-  tool_panel_section_id: variant
-  tool_panel_section_label: Variant Analyses
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: snpsift
-  owner: iuc
+- name: manta
+  owner: artbio
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: snpsift_dbnsfp_generic
+- name: snpeff
   owner: iuc
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
@@ -359,78 +314,78 @@ tools:
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: pindel
-  owner: artbio
+- name: freebayes
+  owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: mutational_patterns
-  owner: artbio
+- name: crossmap_vcf
+  owner: iuc
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: lumpy_smoove
-  owner: artbio
+- name: vcftools_isec
+  owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: artbio_mutect2
-  owner: artbio
+- name: vcffixup
+  owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcfbedintersect
-  owner: devteam
+- name: snpsift_dbnsfp
+  owner: iuc
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcfannotate
-  owner: devteam
+- name: snpsift
+  owner: iuc
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: crossmap_vcf
+- name: snpsift_dbnsfp_generic
   owner: iuc
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: svtyper
-  owner: hepcat72
+- name: pindel
+  owner: artbio
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sigmut
-  owner: artbio
+- name: vcfbedintersect
+  owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcfhethom
+- name: vcfannotate
   owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: manta
-  owner: artbio
+- name: svtyper
+  owner: hepcat72
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: lumpy_sv
+- name: sigmut
   owner: artbio
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcftools_annotate
+- name: vcfhethom
   owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcftools_merge
+- name: vcftools_annotate
   owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gatk2
-  owner: iuc
+- name: vcftools_merge
+  owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -444,11 +399,6 @@ tools:
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: freebayes
-  owner: devteam
-  tool_panel_section_id: variant
-  tool_panel_section_label: Variant Analyses
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: qualimap2_bamqc
   owner: refinery-platform
   tool_panel_section_id: variant
@@ -469,22 +419,7 @@ tools:
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcffilter
-  owner: devteam
-  tool_panel_section_id: variant
-  tool_panel_section_label: Variant Analyses
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcfallelicprimitives
-  owner: devteam
-  tool_panel_section_id: variant
-  tool_panel_section_label: Variant Analyses
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcf2tsv
-  owner: devteam
-  tool_panel_section_id: variant
-  tool_panel_section_label: Variant Analyses
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: variant_select
+- name: variant_select
   owner: devteam
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
@@ -499,33 +434,43 @@ tools:
   tool_panel_section_id: variant
   tool_panel_section_label: Variant Analyses
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: mapping_to_ucsc
-  owner: devteam
+- name: high_dim_heatmap
+  owner: artbio
   tool_panel_section_id: plots
   tool_panel_section_label: Graph/Display Data
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: high_dim_heatmap
-  owner: artbio
+- name: ggplot2_histogram
+  owner: iuc
   tool_panel_section_id: plots
   tool_panel_section_label: Graph/Display Data
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: histogram
+- name: circos
+  owner: iuc
+  tool_panel_section_id: plots
+  tool_panel_section_label: Graph/Display Data
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: proteore_venn_diagram
+  owner: proteore
+  tool_panel_section_id: plots
+  tool_panel_section_label: Graph/Display Data
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: mapping_to_ucsc
   owner: devteam
   tool_panel_section_id: plots
   tool_panel_section_label: Graph/Display Data
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: ggplot2_histogram
-  owner: iuc
+- name: histogram
+  owner: devteam
   tool_panel_section_id: plots
   tool_panel_section_label: Graph/Display Data
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: spades
-  owner: nml
+- name: sr_bowtie
+  owner: artbio
   tool_panel_section_id: metavisitor_2
   tool_panel_section_label: Metavisitor-2
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blast_to_scaffold
-  owner: artbio
+- name: spades
+  owner: nml
   tool_panel_section_id: metavisitor_2
   tool_panel_section_label: Metavisitor-2
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -534,37 +479,72 @@ tools:
   tool_panel_section_id: metavisitor_2
   tool_panel_section_label: Metavisitor-2
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blastparser_and_hits
-  owner: artbio
-  tool_panel_section_id: metavisitor_2
-  tool_panel_section_label: Metavisitor-2
+- name: scipy_sparse
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: oases
-  owner: artbio
-  tool_panel_section_id: metavisitor_2
-  tool_panel_section_label: Metavisitor-2
+- name: keras_model_builder
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: small_rna_maps
-  owner: artbio
-  tool_panel_section_id: metavisitor_2
-  tool_panel_section_label: Metavisitor-2
+- name: sklearn_searchcv
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sr_bowtie
-  owner: artbio
-  tool_panel_section_id: metavisitor_2
-  tool_panel_section_label: Metavisitor-2
+- name: sklearn_train_test_eval
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sequence_format_converter
-  owner: artbio
-  tool_panel_section_id: metavisitor_2
-  tool_panel_section_label: Metavisitor-2
+- name: sklearn_stacking_ensemble_models
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fetch_fasta_from_ncbi
-  owner: artbio
-  tool_panel_section_id: metavisitor_2
-  tool_panel_section_label: Metavisitor-2
+- name: sklearn_sample_generator
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: plotly_regression_performance_plots
+- name: sklearn_regression_metrics
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_pairwise_metrics
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_numeric_clustering
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_nn_classifier
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_model_validation
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_generalized_linear
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_feature_selection
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_estimator_attributes
   owner: bgruening
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
@@ -574,32 +554,77 @@ tools:
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: summary_statistics
-  owner: vmarcon
-  tool_panel_section_id: stats
-  tool_panel_section_label: Statistics
+- name: sklearn_discriminant_classifier
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deseq2
+- name: sklearn_clf_metrics
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: plotly_parallel_coordinates_plot
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: plotly_ml_performance_plots
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_svm_classifier
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_data_preprocess
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sklearn_build_pipeline
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: keras_model_config
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: model_prediction
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: keras_batch_models
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: plotly_regression_performance_plots
+  owner: bgruening
+  tool_panel_section_id: machine_learning
+  tool_panel_section_label: Machine Learning
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: table_compute
   owner: iuc
   tool_panel_section_id: stats
   tool_panel_section_label: Statistics
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: regex_find_replace
-  owner: galaxyp
-  tool_panel_section_id: textutil
-  tool_panel_section_label: Text Manipulation
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: merge_columns_with_delimiter
-  owner: saket-choudhary
-  tool_panel_section_id: textutil
-  tool_panel_section_label: Text Manipulation
+- name: summary_statistics
+  owner: vmarcon
+  tool_panel_section_id: stats
+  tool_panel_section_label: Statistics
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: datamash_reverse
   owner: iuc
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: datamash_transpose
+- name: filter_tabular
   owner: iuc
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
@@ -609,13 +634,13 @@ tools:
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: replace_chromosome_names
-  owner: earlhaminst
+- name: add_column_headers
+  owner: estrain
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: filter_tabular
-  owner: iuc
+- name: text_processing
+  owner: bgruening
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -624,16 +649,21 @@ tools:
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: regex_replace
-  owner: kellrott
+- name: cut_columns
+  owner: devteam
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: text_processing
+- name: replace_column_by_key_value_file
   owner: bgruening
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: merge_columns_with_delimiter
+  owner: saket-choudhary
+  tool_panel_section_id: textutil
+  tool_panel_section_label: Text Manipulation
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: tabular_to_csv
   owner: mnhn65mo
   tool_panel_section_id: textutil
@@ -644,43 +674,43 @@ tools:
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: transpose
-  owner: jmsong
+- name: regex_find_replace
+  owner: galaxyp
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: tables_arithmetic_operations
-  owner: devteam
+- name: datamash_transpose
+  owner: iuc
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: column_regex_substitution
-  owner: blankenberg
+- name: transpose
+  owner: jmsong
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: mapping_quality_stats
-  owner: artbio
-  tool_panel_section_id: sam/bam_manipulation
-  tool_panel_section_label: SAM/BAM manipulation
+- name: tables_arithmetic_operations
+  owner: devteam
+  tool_panel_section_id: textutil
+  tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sambamba
-  owner: artbio
+- name: bamtools
+  owner: devteam
   tool_panel_section_id: sam/bam_manipulation
   tool_panel_section_label: SAM/BAM manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: crossmap_bam
-  owner: iuc
+- name: bamtools_split
+  owner: devteam
   tool_panel_section_id: sam/bam_manipulation
   tool_panel_section_label: SAM/BAM manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: pe_histogram
-  owner: iuc
+- name: mapping_quality_stats
+  owner: artbio
   tool_panel_section_id: sam/bam_manipulation
   tool_panel_section_label: SAM/BAM manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bamtools
-  owner: devteam
+- name: sambamba
+  owner: artbio
   tool_panel_section_id: sam/bam_manipulation
   tool_panel_section_label: SAM/BAM manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -689,32 +719,22 @@ tools:
   tool_panel_section_id: sam/bam_manipulation
   tool_panel_section_label: SAM/BAM manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bamtools_split
-  owner: devteam
-  tool_panel_section_id: sam/bam_manipulation
-  tool_panel_section_label: SAM/BAM manipulation
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sambamba_filter
-  owner: lomereiter
+- name: pe_histogram
+  owner: iuc
   tool_panel_section_id: sam/bam_manipulation
   tool_panel_section_label: SAM/BAM manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deeptools_bam_coverage
-  owner: bgruening
-  tool_panel_section_id: deeptools
-  tool_panel_section_label: DEEPTOOLS
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deeptools_compute_gc_bias
+- name: deeptools_plot_coverage
   owner: bgruening
   tool_panel_section_id: deeptools
   tool_panel_section_label: DEEPTOOLS
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deeptools_alignmentsieve
+- name: deeptools_correct_gc_bias
   owner: bgruening
   tool_panel_section_id: deeptools
   tool_panel_section_label: DEEPTOOLS
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deeptools_correct_gc_bias
+- name: deeptools_compute_gc_bias
   owner: bgruening
   tool_panel_section_id: deeptools
   tool_panel_section_label: DEEPTOOLS
@@ -724,7 +744,7 @@ tools:
   tool_panel_section_id: deeptools
   tool_panel_section_label: DEEPTOOLS
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deeptools_plot_coverage
+- name: deeptools_bam_coverage
   owner: bgruening
   tool_panel_section_id: deeptools
   tool_panel_section_label: DEEPTOOLS
@@ -749,117 +769,117 @@ tools:
   tool_panel_section_id: riboprofiling
   tool_panel_section_label: Ribosome Profiling
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_stats
+- name: bcftools_view
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_cnv
+- name: bcftools_stats
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bowtie2
-  owner: devteam
+- name: bcftools_roh
+  owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_consensus
+- name: bcftools_reheader
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcfsort
-  owner: devteam
+- name: bcftools_query_list_samples
+  owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vcfvcfintersect
-  owner: devteam
+- name: bcftools_query
+  owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_isec
+- name: bcftools_plugin_tag2tag
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_call
+- name: bcftools_plugin_setgt
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_color_chrs
+- name: bcftools_plugin_missing2ref
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_frameshifts
+- name: bcftools_plugin_mendelian
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_setgt
+- name: bcftools_plugin_impute_info
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_gtcheck
+- name: bcftools_plugin_frameshifts
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_tag2tag
+- name: bcftools_plugin_fixploidy
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_merge
+- name: bcftools_plugin_fill_tags
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_counts
+- name: bcftools_plugin_fill_an_ac
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_csq
+- name: bcftools_plugin_dosage
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_fill_tags
+- name: bcftools_plugin_counts
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_impute_info
+- name: bcftools_plugin_color_chrs
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_query_list_samples
+- name: bcftools_norm
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_fill_an_ac
+- name: bcftools_mpileup
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_norm
+- name: bcftools_merge
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_convert_from_vcf
+- name: bcftools_isec
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_mendelian
+- name: bcftools_gtcheck
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
@@ -869,7 +889,7 @@ tools:
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_dosage
+- name: bcftools_csq
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
@@ -879,48 +899,48 @@ tools:
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_reheader
+- name: bcftools_convert_from_vcf
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_concat
+- name: bcftools_consensus
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_fixploidy
+- name: bcftools_concat
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_plugin_missing2ref
+- name: bcftools_cnv
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_mpileup
+- name: bcftools_call
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_query
+- name: bcftools_annotate
   owner: iuc
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_roh
-  owner: iuc
+- name: bowtie2
+  owner: devteam
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_annotate
-  owner: iuc
+- name: vcfsort
+  owner: devteam
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bcftools_view
-  owner: iuc
+- name: vcfvcfintersect
+  owner: devteam
   tool_panel_section_id: bcftools
   tool_panel_section_label: BCFtools
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -929,28 +949,28 @@ tools:
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: collection_element_identifiers
-  owner: iuc
+- name: concatenate_multiple_datasets
+  owner: artbio
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: extract_element_from_collection
-  owner: erasmus-medical-center
+- name: bundle_collections
+  owner: nml
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: concatenate_multiple_datasets
-  owner: artbio
+- name: collection_element_identifiers
+  owner: iuc
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: collection_column_join
-  owner: iuc
+- name: extract_element_from_collection
+  owner: erasmus-medical-center
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bundle_collections
-  owner: nml
+- name: collection_column_join
+  owner: iuc
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -959,13 +979,13 @@ tools:
   tool_panel_section_id: getext
   tool_panel_section_label: Get Data
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: show_metadata
-  owner: yhoogstrate
+- name: get_reference_fasta
+  owner: artbio
   tool_panel_section_id: getext
   tool_panel_section_label: Get Data
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: get_reference_fasta
-  owner: artbio
+- name: show_metadata
+  owner: yhoogstrate
   tool_panel_section_id: getext
   tool_panel_section_label: Get Data
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -974,35 +994,50 @@ tools:
   tool_panel_section_id: gatktools
   tool_panel_section_label: GATKtools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bigwig_to_bedgraph
-  owner: artbio
+- name: crossmap_bam
+  owner: iuc
   tool_panel_section_id: convert
   tool_panel_section_label: Convert Formats
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gtftobed12
+- name: crossmap_wig
   owner: iuc
   tool_panel_section_id: convert
   tool_panel_section_label: Convert Formats
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sequence_format_converter
+- name: bigwig_to_wig
   owner: artbio
   tool_panel_section_id: convert
   tool_panel_section_label: Convert Formats
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: crossmap_wig
+- name: bigwig_to_bedgraph
+  owner: artbio
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: annotatemyids
   owner: iuc
   tool_panel_section_id: convert
   tool_panel_section_label: Convert Formats
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: proteore_venn_diagram
-  owner: proteore
-  tool_panel_section_id: group
-  tool_panel_section_label: Join, Subtract and Group
+- name: vcf2maf
+  owner: iuc
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: cherry_pick_fasta
+- name: gtftobed12
+  owner: iuc
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: sequence_format_converter
   owner: artbio
-  tool_panel_section_id: fasta_manipulation
-  tool_panel_section_label: Fasta Manipulation
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: intersect
+  owner: devteam
+  tool_panel_section_id: bxops
+  tool_panel_section_label: Operate on Genomic Intervals
   tool_shed_url: toolshed.g2.bx.psu.edu
 - name: fasta_filter_by_length
   owner: devteam
@@ -1024,26 +1059,36 @@ tools:
   tool_panel_section_id: fasta_manipulation
   tool_panel_section_label: Fasta Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: edger
-  owner: iuc
+- name: gsc_center_scale
+  owner: artbio
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential expression
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: htseq_count
-  owner: lparsons
+- name: featurecounts
+  owner: iuc
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential expression
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: featurecounts
+- name: edger
   owner: iuc
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential expression
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: hisat2
+- name: deseq2
   owner: iuc
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential expression
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: cpm_tpm_rpk
+  owner: artbio
+  tool_panel_section_id: differential_expression
+  tool_panel_section_label: Differential expression
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: htseq_count
+  owner: lparsons
+  tool_panel_section_id: differential_expression
+  tool_panel_section_label: Differential expression
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: ncbi_blast_plus
   owner: devteam
   tool_panel_section_id: ncbi_blast_plus
@@ -1064,6 +1109,11 @@ tools:
   tool_panel_section_id: ngs:_assembly
   tool_panel_section_label: 'NGS: Assembly'
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: lumpy_smoove
+  owner: artbio
+  tool_panel_section_id: genomic_variants
+  tool_panel_section_label: Genomic Variants
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: varscan_vaf
   owner: artbio
   tool_panel_section_id: genomic_variants
@@ -1089,147 +1139,137 @@ tools:
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: snpeff
-  owner: iuc
-  tool_panel_section_id: genomic_variants
-  tool_panel_section_label: Genomic Variants
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: rsem
+- name: small_rna_signatures
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: mircounts
+- name: rsem
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: probecoverage
-  owner: artbio
+- name: rseqc
+  owner: nilesh
   tool_panel_section_id: ngs:_mapping
   tool_panel_section_label: 'NGS: Mapping'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blastparser_and_hits
+- name: fetch_fasta_from_ncbi
   owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blast_to_scaffold
+- name: blastx_to_scaffold
   owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fetch_fasta_from_ncbi
+- name: blastparser_and_hits
   owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: vsearch
-  owner: iuc
+- name: blast_unmatched
+  owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: regex_find_replace
-  owner: galaxyp
+- name: blast_to_scaffold
+  owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blast_unmatched
-  owner: artbio
+- name: vsearch
+  owner: iuc
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: samtools_flagstat
-  owner: devteam
-  tool_panel_section_id: ngs:_sam_tools
-  tool_panel_section_label: 'NGS: SAM Tools'
-  tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_burden
+- name: gemini_stats
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_inheritance
+- name: gemini_set_somatic
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_stats
+- name: gemini_query
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_query
+- name: gemini_pathways
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_db_info
+- name: gemini_lof_sieve
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_actionable_mutations
+- name: gemini_load
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_annotate
+- name: gemini_inheritance
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_roh
+- name: gemini_gene_wise
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_gene_wise
+- name: gemini_db_info
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_amend
+- name: gemini_burden
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_interactions
+- name: gemini_actionable_mutations
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_windower
+- name: gemini_annotate
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_qc
+- name: gemini_roh
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_lof_sieve
+- name: gemini_amend
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_pathways
+- name: gemini_interactions
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_fusions
+- name: gemini_windower
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_load
+- name: gemini_qc
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gemini_set_somatic
+- name: gemini_fusions
   owner: iuc
   tool_panel_section_id: gemini
   tool_panel_section_label: Gemini Suite
@@ -1244,31 +1284,31 @@ tools:
   tool_panel_section_id: vcftools
   tool_panel_section_label: vcftools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: star_fusion
+- name: arriba_get_filters
   owner: iuc
   tool_panel_section_id: gene_fusions
   tool_panel_section_label: Gene Fusions
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: arriba_download_reference
-  owner: jjohnson
-  tool_panel_section_id: gene_fusions
-  tool_panel_section_label: Gene Fusions
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: arriba_draw_fusions
-  owner: jjohnson
+  owner: iuc
   tool_panel_section_id: gene_fusions
   tool_panel_section_label: Gene Fusions
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: arriba_get_filters
-  owner: jjohnson
+- name: arriba
+  owner: iuc
   tool_panel_section_id: gene_fusions
   tool_panel_section_label: Gene Fusions
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: arriba
-  owner: jjohnson
+- name: star_fusion
+  owner: iuc
   tool_panel_section_id: gene_fusions
   tool_panel_section_label: Gene Fusions
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: delly_filter
+  owner: iuc
+  tool_panel_section_id: cnv
+  tool_panel_section_label: CNV
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: delly_merge
   owner: iuc
   tool_panel_section_id: cnv
@@ -1279,7 +1319,7 @@ tools:
   tool_panel_section_id: cnv
   tool_panel_section_label: CNV
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: delly_filter
+- name: delly_cnv
   owner: iuc
   tool_panel_section_id: cnv
   tool_panel_section_label: CNV
@@ -1294,7 +1334,7 @@ tools:
   tool_panel_section_id: cnv
   tool_panel_section_label: CNV
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: delly_cnv
+- name: cnvkit_access
   owner: iuc
   tool_panel_section_id: cnv
   tool_panel_section_label: CNV
@@ -1314,58 +1354,58 @@ tools:
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_gatk_picard_index_builder
+- name: data_manager_bwa_mem_index_builder
   owner: devteam
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_twobit_builder
+- name: data_manager_fetch_genome_dbkeys_all_fasta
   owner: devteam
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: data_manager_hisat2_index_builder
+  owner: iuc
+  tool_panel_section_id: None
+  tool_panel_section_label: None
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: data_manager_sam_fasta_index_builder
   owner: devteam
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_gemini_database_downloader
+- name: data_manager_snpeff
   owner: iuc
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_bowtie2_index_builder
-  owner: devteam
+- name: data_manager_vep_cache_downloader
+  owner: iuc
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_bwa_mem_index_builder
+- name: data_manager_bowtie2_index_builder
   owner: devteam
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_fetch_genome_dbkeys_all_fasta
+- name: data_manager_gatk_picard_index_builder
   owner: devteam
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_hisat2_index_builder
+- name: data_manager_gemini_database_downloader
   owner: iuc
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_snpeff
+- name: data_manager_snpsift_dbnsfp
   owner: iuc
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_star_index_builder
-  owner: iuc
+- name: data_manager_twobit_builder
+  owner: devteam
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: data_manager_snpsift_dbnsfp
-  owner: iuc
-  tool_panel_section_id: None
-  tool_panel_section_label: None
-  tool_shed_url: toolshed.g2.bx.psu.edu
\ No newline at end of file
diff --git a/environments/Conect/files/galaxy/config/job_conf.xml b/environments/Conect/files/galaxy/config/job_conf.xml
deleted file mode 100644
index ea5aea1..0000000
--- a/environments/Conect/files/galaxy/config/job_conf.xml
+++ /dev/null
@@ -1,157 +0,0 @@
-<?xml version="1.0"?>
-<!-- Do not modify this file, it will we overwritten by ansible galaxykickstart -->
-<job_conf>
-    <plugins workers="4">
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
-        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
-            <param id="drmaa_library_path">/usr/lib/slurm-drmaa/lib/libdrmaa.so</param>
-        </plugin>
-    </plugins>
-
-    <handlers assign_with="db-skip-locked" default="handlers">
-        <handler id="handler_0" tags="handlers"/>
-        <handler id="handler_1" tags="handlers"/>
-        <handler id="handler_2" tags="handlers"/>
-        <handler id="handler_3" tags="handlers"/>
-    </handlers>
-
-    <destinations default="slurm_cluster">
-        <destination id="slurm_cluster" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=1 --share</param>
-        </destination>
-        <destination id="slurm_cluster_2" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=2 --share</param>
-        </destination>
-        <destination id="slurm_cluster_4" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=4 --share</param>
-        </destination>
-        <destination id="slurm_cluster_8" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=8 --share</param>
-        </destination>
-        <destination id="slurm_cluster_16" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=16 --share</param>
-        </destination>
-        <destination id="java_cluster" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <env id="_JAVA_OPTIONS">-Xmx40g</env>
-            <env id="_JAVA_OPTIONS">-Xms512m</env>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=1 --share</param>
-        </destination>
-        <destination id="slurm_upload" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=1 --share</param>
-        </destination>
-        <destination id="disk_intensive" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=8 --share</param>
-        </destination>
-        <destination id="varscan" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=1 --share</param>
-        </destination>
-        <destination id="smoove" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=8 --share</param>
-        </destination>
-        <destination id="vcfvcfintersect" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=8 --share</param>
-        </destination>
-        <destination id="artbio_bam_cleaning" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=2 --share</param>
-        </destination>
-
-    </destinations>
-    <limits>
-        <limit type="anonymous_user_concurrent_jobs">1</limit>
-        <limit type="destination_user_concurrent_jobs" id="slurm_cluster">60</limit>
-        <limit type="destination_user_concurrent_jobs" id="slurm_cluster_2">50</limit>
-        <limit type="destination_user_concurrent_jobs" id="slurm_cluster_4">18</limit>
-        <limit type="destination_user_concurrent_jobs" id="slurm_cluster_8">8</limit>
-        <limit type="destination_user_concurrent_jobs" id="slurm_cluster_16">4</limit>
-        <limit type="destination_user_concurrent_jobs" id="slurm_upload">4</limit>
-        <limit type="destination_user_concurrent_jobs" id="java_cluster">35</limit>
-        <limit type="destination_user_concurrent_jobs" id="disk_intensive">4</limit>
-        <limit type="destination_user_concurrent_jobs" id="varscan">25</limit>
-        <limit type="destination_user_concurrent_jobs" id="smoove">8</limit>
-        <limit type="destination_user_concurrent_jobs" id="vcfvcfintersect">6</limit>
-        <limit type="destination_user_concurrent_jobs" id="artbio_bam_cleaning">16</limit>
-
-        <limit type="destination_total_concurrent_jobs" id="slurm_cluster">60</limit>
-        <limit type="destination_total_concurrent_jobs" id="slurm_cluster_2">50</limit>
-        <limit type="destination_total_concurrent_jobs" id="slurm_cluster_4">18</limit>
-        <limit type="destination_total_concurrent_jobs" id="slurm_cluster_8">8</limit>
-        <limit type="destination_total_concurrent_jobs" id="slurm_cluster_16">4</limit>
-        <limit type="destination_total_concurrent_jobs" id="slurm_upload">8</limit>
-        <limit type="destination_user_concurrent_jobs" id="java_cluster">35</limit>
-        <limit type="destination_total_concurrent_jobs" id="disk_intensive">4</limit>
-        <limit type="destination_total_concurrent_jobs" id="varscan">25</limit>
-        <limit type="destination_total_concurrent_jobs" id="smoove">12</limit>
-        <limit type="destination_total_concurrent_jobs" id="vcfvcfintersect">6</limit>
-        <limit type="destination_total_concurrent_jobs" id="artbio_bam_cleaning">16</limit>
-    </limits>
-    <tools>
-        <tool id="upload1" destination="slurm_upload"/>
-        <tool id="retrieve_fasta_from_NCBI" destination="slurm_cluster_4"/>
-        <tool id="trimmomatic" destination="slurm_cluster_8"/>
-        <tool id="Group" destination="slurm_cluster"/>
-        <tool id="bcftools_annotate" destination="java_cluster"/>
-        <tool id="bcftools_mpileup" destination="slurm_cluster_16"/>
-        <tool id="bowtieForSmallRNA" destination="slurm_cluster_16"/>
-        <tool id="trinity" destination="slurm_cluster_16"/>
-        <tool id="spades" destination="slurm_cluster_16"/>
-        <tool id="bowtie2" destination="slurm_cluster_16"/>
-        <tool id="bwa_mem" destination="slurm_cluster_16"/>
-        <tool id="bwa" destination="slurm_cluster_16"/>
-        <tool id="hisat2" destination="slurm_cluster_8"/>
-        <tool id="rna_star" destination="slurm_cluster_8"/>
-        <tool id="arriba" destination="slurm_cluster_8"/>
-        <tool id="star_fusion" destination="slurm_cluster_8"/>
-        <tool id="featurecounts" destination="slurm_cluster_8"/>
-        <tool id="ncbi_blastn_wrapper" destination="slurm_cluster_16"/>
-        <tool id="ncbi_blastx_wrapper" destination="slurm_cluster_16"/>
-        <tool id="ncbi_tblastx_wrapper" destination="slurm_cluster_16"/>
-        <tool id="ncbi_tblastn_wrapper" destination="slurm_cluster_16"/>
-        <tool id="khmer_normalize_by_median" destination="slurm_cluster_16"/>
-        <tool id="deeptools_bam_coverage" destination="slurm_cluster_4"/>
-        <tool id="deeptools_plot_coverage" destination="slurm_cluster_16"/>
-        <tool id="lumpy" destination="disk_intensive"/>
-        <tool id="lumpy_smoove" destination="smoove"/>
-        <tool id="varscan_somatic" destination="varscan"/>
-        <tool id="freebayes" destination="slurm_cluster_16"/>
-        <tool id="manta" destination="slurm_cluster_8"/>
-        <tool id="sam_to_bam" destination="slurm_cluster_8"/>
-        <tool id="sambamba_sample_or_filter" destination="slurm_cluster_8"/>
-        <tool id="artbio_bam_cleaning" destination="artbio_bam_cleaning"/>
-        <tool id="picard_MarkDuplicates" destination="java_cluster"/>
-        <tool id="picard_ReplaceSamHeader" destination="java_cluster"/>
-        <tool id="snpsift" destination="java_cluster"/>
-        <tool id="snpSift_annotate" destination="java_cluster"/>
-        <tool id="snpEff" destination="java_cluster"/>
-        <tool id="mutect2" destination="java_cluster"/>
-        <tool id="samtools_slice_bam" destination="slurm_cluster_8"/>
-        <tool id="samtools_fastx" destination="slurm_cluster_4"/>
-        <tool id="samtool_filter2" destination="slurm_cluster_4"/>
-        <tool id="mutational_patterns" destination="slurm_cluster_2"/>
-        <tool id="samtools_calmd" destination="slurm_cluster_4"/>
-        <tool id="vcfvcfintersect" destination="vcfvcfintersect"/>
-    </tools>
-</job_conf>
\ No newline at end of file
diff --git a/environments/Conect/files/galaxy/config/job_conf.yml b/environments/Conect/files/galaxy/config/job_conf.yml
new file mode 100644
index 0000000..904b4e4
--- /dev/null
+++ b/environments/Conect/files/galaxy/config/job_conf.yml
@@ -0,0 +1,249 @@
+# This file is managed by Ansible.
+# Do not edit this file manually. Any changes will be automatically reverted.
+
+runners:
+  local_runner:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 8
+  slurm:
+    load: galaxy.jobs.runners.slurm:SlurmJobRunner
+    drmaa_library_path: /usr/lib/slurm-drmaa/lib/libdrmaa.so
+
+handling:
+  assign:
+    - db-skip-locked
+  processes:
+    handler0:
+    handler1:
+    handler2:
+    handler3:
+
+execution:
+  default: cluster_1
+  environments:
+    local_env:
+      runner: local_runner
+      tmp_dir: true
+    gce_multicore:
+      runner: local_runner
+      local_slots: 2
+      embed_metadata_in_job: true
+    cluster_1:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=1"
+    cluster_2:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=2"
+    cluster_4:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=4"
+    cluster_8:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=8"
+    cluster_16:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=16"
+    java_cluster:
+      runner: slurm # if not working, try drmaa runner
+      nativeSpecification: "--partition=debug --ntasks=1"
+      env:
+        - name: '_JAVA_OPTIONS'
+          value: '-Xmx40g -Xms512m'
+        - file: '/home/galaxy/galaxy/.venv/bin/activate'
+    slurm_upload:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=1"
+    disk_intensive:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=8"
+    varscan:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=1"
+    smoove:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=8"
+    vcfvcfintersect:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=8"
+    artbio_bam_cleaning:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=4"
+
+limits:
+  - type: anonymous_user_concurrent_jobs
+    value: 1
+  - type: registered_user_concurrent_jobs
+    value: 70
+
+  - type: environment_total_concurrent_jobs
+    id: cluster_1
+    value: 80
+  - type: environment_total_concurrent_jobs
+    id: cluster_2
+    value: 50
+  - type: environment_total_concurrent_jobs
+    id: cluster_4
+    value: 18
+  - type: environment_total_concurrent_jobs
+    id: cluster_8
+    value: 10
+  - type: environment_total_concurrent_jobs
+    id: cluster_16
+    value: 5
+  - type: environment_total_concurrent_jobs
+    id: java_cluster
+    value: 35
+  - type: environment_total_concurrent_jobs
+    id: slurm_upload
+    value: 16
+  - type: environment_total_concurrent_jobs
+    id: disk_intensive
+    value: 4
+  - type: environment_total_concurrent_jobs
+    id: smoove
+    value: 8
+  - type: environment_total_concurrent_jobs
+    id: vcfvcfintersect
+    value: 6
+  - type: environment_total_concurrent_jobs
+    id: artbio_bam_cleaning
+    value: 4
+
+tools:
+  - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
+    environment: local_env
+
+  - id: "arriba"
+    destination: "cluster_8"
+
+  - id: "artbio_bam_cleaning"
+    destination: "artbio_bam_cleaning"
+
+  - id: "bcftools_annotate"
+    destination: "java_cluster"
+
+  - id: "bcftools_mpileup"
+    destination: "cluster_16"
+
+  - id: "bowtie2"
+    destination: "cluster_16"
+
+  - id: "bowtieForSmallRNA"
+    destination: "cluster_16"
+
+  - id: "bwa_mem"
+    destination: "cluster_16"
+
+  - id: "bwa"
+    destination: "cluster_16"
+
+  - id: "deeptools_bam_coverage"
+    destination: "cluster_4"
+
+  - id: "deeptools_plot_coverage"
+    destination: "cluster_16"
+
+  - id: "featurecounts"
+    destination: "cluster_8"
+
+  - id: "freebayes"
+    destination: "cluster_16"
+
+  - id: "Group"
+    destination: "cluster_1"
+
+  - id: "hisat2"
+    destination: "cluster_8"
+
+  - id: "khmer_normalize_by_median"
+    destination: "cluster_16"
+
+  - id: "lumpy_smoove"
+    destination: "smoove"
+
+  - id: "lumpy"
+    destination: "disk_intensive"
+
+  - id: "manta"
+    destination: "cluster_8"
+
+  - id: "mutational_patterns"
+    destination: "cluster_2"
+
+  - id: "mutect2"
+    destination: "java_cluster"
+
+  - id: "ncbi_blastn_wrapper"
+    destination: "cluster_16"
+
+  - id: "ncbi_blastx_wrapper"
+    destination: "cluster_16"
+
+  - id: "ncbi_tblastn_wrapper"
+    destination: "cluster_16"
+
+  - id: "ncbi_tblastx_wrapper"
+    destination: "cluster_16"
+
+  - id: "picard_MarkDuplicates"
+    destination: "java_cluster"
+
+  - id: "picard_ReplaceSamHeader"
+    destination: "java_cluster"
+
+  - id: "retrieve_fasta_from_NCBI"
+    destination: "cluster_4"
+
+  - id: "rna_star"
+    destination: "cluster_8"
+
+  - id: "sam_to_bam"
+    destination: "cluster_8"
+
+  - id: "sambamba_sample_or_filter"
+    destination: "cluster_4"
+
+  - id: "samtool_filter2"
+    destination: "cluster_4"
+
+  - id: "samtools_calmd"
+    destination: "cluster_4"
+
+  - id: "samtools_fastx"
+    destination: "cluster_4"
+
+  - id: "samtools_slice_bam"
+    destination: "cluster_8"
+
+  - id: "snpEff"
+    destination: "java_cluster"
+
+  - id: "snpSift_annotate"
+    destination: "java_cluster"
+
+  - id: "snpsift"
+    destination: "java_cluster"
+
+  - id: "spades"
+    destination: "cluster_16"
+
+  - id: "star_fusion"
+    destination: "cluster_8"
+
+  - id: "trimmomatic"
+    destination: "cluster_8"
+
+  - id: "trinity"
+    destination: "cluster_16"
+
+  - id: "upload1"
+    destination: "slurm_upload"
+
+  - id: "varscan_somatic"
+    destination: "varscan"
+
+  - id: "vcf2maf"
+    destination: "cluster_4"
+
+  - id: "vcfvcfintersect"
+    destination: "vcfvcfintersect"
diff --git a/environments/Conect/group_vars/all/galaxy b/environments/Conect/group_vars/all/galaxy
index d0d4f36..18a7327 100644
--- a/environments/Conect/group_vars/all/galaxy
+++ b/environments/Conect/group_vars/all/galaxy
@@ -1,27 +1,29 @@
 ---
-# overwrite properly the previous uwgi-based galaxykickstart (default: no)
 # Galaxy
 galaxy_additional_venv_packages: drmaa
+galaxy_commit_id: release_23.0
+galaxy_config_dir: "{{ galaxy_server_dir }}/config"
+galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
 galaxy_create_user: true
-galaxy_separate_privileges: true
-galaxy_privsep_user: "{{ galaxy_user }}"
+galaxy_force_checkout: true
 galaxy_layout: legacy
-galaxy_server_dir: "{{ galaxy_root }}/galaxy"
-galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
+galaxy_manage_cleanup: yes  # Install a cron job to clean up Galaxy framework and job execution temporary
 galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
-galaxy_config_dir: "{{ galaxy_server_dir }}/config"
-galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
+galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
+galaxy_privsep_user: "{{ galaxy_user }}"
 galaxy_root: /home/galaxy
-galaxy_user: {name: galaxy, shell: /bin/bash}
-galaxy_commit_id: release_22.05
-galaxy_force_checkout: true
+galaxy_separate_privileges: true
+galaxy_server_dir: "{{ galaxy_root }}/galaxy"
 galaxy_tool_dependency_dir: "{{ galaxy_root }}/tool_dependencies"
-galaxy_manage_cleanup: yes  # Install a cron job to clean up Galaxy framework and job execution temporary
+galaxy_user: {name: galaxy, shell: /bin/bash}
+miniconda_channels: ['conda-forge', 'bioconda', 'defaults']
 miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
-miniconda_version: 4.7.12
-miniconda_manage_dependencies: false
+miniconda_version: 23.9
+
 galaxy_config:
   galaxy:
+    brand: "🧬 CONECT-AML"
+    builds_file_path: shared/ucsc/builds.txt
     admin_users: !vault |
           $ANSIBLE_VAULT;1.1;AES256
           66646635666564653662306436393231646231613062623864363336653436343037613430383731
@@ -31,27 +33,21 @@ galaxy_config:
           61386438623862346534366235383230633961346533313361656163646163616636643164623338
           39623835333062623464366237336666376564323934623863656565393962346432616365383134
           663633653163316536633865663735366636
-    allow_library_path_paste: true
-    allow_user_dataset_purge: true
-    allow_user_deletion: true
-    allow_user_impersonation: true
-    brand: "🧬 CONECT-AML"
-    builds_file_path: shared/ucsc/builds.txt
-    container_resolvers_config_file: ''
-    data_dir: /home/galaxy/galaxy/database
-    data_manager_config_file: /home/galaxy/galaxy/config/data_manager_conf.xml.sample
-    database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
-    datatypes_config_file: /home/galaxy/galaxy/config/datatypes_conf.xml.sample
-    dependency_resolvers_config_file: /home/galaxy/galaxy/config/dependency_resolvers_conf.xml
     display_servers: hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
-    email_from: !vault |
+    smtp_username: !vault |
           $ANSIBLE_VAULT;1.1;AES256
-          32353333616334313863356663386539653965653938316431613836636663373631646563356638
-          3737376464376539653361386464613666313761613535350a623364613262306233623634303930
-          34386439373763363139383033633233323065363235383138616133333163663935636665383635
-          3639353162643966340a333632323262643961616537393665353334323061383762363365623830
-          37393165393531343530376461623564393164376432333430333164393762343136
-    enable_quotas: true
+          37616437306334383436313638346266303234646532313263393764393233613361656635616261
+          3336326132616166313134343336303033623966646333370a363135323331353234316431333334
+          33356432346431656636623765363534326237363239643164373830343535346533366331663731
+          6431323561643936330a333939333931633831326133303236353136623138373832383236656462
+          37656139313564376430316133306431313662623463383161376262356263633736
+    smtp_password: !vault |
+          $ANSIBLE_VAULT;1.1;AES256
+          66613031386130396336353334633034653037653336633937386363386233656162396135343663
+          6330363437613665383432626539303330333734633636370a363634353439643030383035636364
+          39393036316235653239633839333032306537356535633334613931343036346461656165616434
+          6330646264373937310a306164643834633230333739643932643961666163313066373162346535
+          35303831363863616134636639306136303934376566383436353833333930383732
     error_email_to: !vault |
           $ANSIBLE_VAULT;1.1;AES256
           61313639613032383335326435633237323162663132303531333066343963373461303733366130
@@ -59,12 +55,17 @@ galaxy_config:
           34363262396431653962616135666333303332633733316665363139303436396230616435656665
           3230336531353130350a663963346161313462336139663630386334323663373463666632363730
           61303862623266383563326261393066336436653864613964376331343764333138
-    expose_dataset_path: true
-    expose_potentially_sensitive_job_metrics: true
-    external_service_type_config_file: /home/galaxy/galaxy/config/external_service_types_conf.xml.sample
+    email_from: !vault |
+          $ANSIBLE_VAULT;1.1;AES256
+          32353333616334313863356663386539653965653938316431613836636663373631646563356638
+          3737376464376539653361386464613666313761613535350a623364613262306233623634303930
+          34386439373763363139383033633233323065363235383138616133333163663935636665383635
+          3639353162643966340a333632323262643961616537393665353334323061383762363365623830
+          37393165393531343530376461623564393164376432333430333164393762343136
+    smtp_server: 'smtp.gmail.com:587'
+    database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
     file_path: datasets
-    ftp_upload_dir: /home/galaxy/galaxy/database/ftp
-    ftp_upload_site: ftp://134.157.183.195
+    object_store_store_by: id
     id_secret: !vault |
           $ANSIBLE_VAULT;1.1;AES256
           36653663383138333461313134343739656536623933336263663261653963333736653335653632
@@ -73,47 +74,47 @@ galaxy_config:
           6430383861643836300a333439383837653466613735393662623637323265383035663732356163
           62333430633636663632373639663865626263633237656339353830343334336534663061623061
           6636366361643132663339333535343462653261636436663531
-    integrated_tool_panel_config: /home/galaxy/galaxy/config/integrated_tool_panel.xml
-    job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
-    job_metrics_config_file: /home/galaxy/galaxy/config/job_metrics_conf.xml
-    job_working_directory: /home/galaxy/galaxy/database/jobs
-    len_file_path: /home/galaxy/galaxy/config/len
-    migrated_tools_config: /home/galaxy/galaxy/config/migrated_tools_conf.xml
+    check_migrate_tools: false
+    tool_data_path: "{{ galaxy_server_dir }}/tool-data"
+    job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
+    allow_library_path_paste: true
+    watch_tool_data_dir: true
+    # File serving perfomance
     nginx_x_accel_redirect_base: /_x_accel_redirect
-    object_store_store_by: id
-    openid_config_file: /home/galaxy/galaxy/config/openid_conf.xml.sample
+    # SQL Performance
+    slow_query_log_threshold: 5
+    enable_per_request_sql_debugging: true
+    # Automation / Ease of Use / User-facing features
+    allow_user_dataset_purge: true
+    enable_quotas: true
+    allow_user_deletion: true
+    allow_user_impersonation: true
+    watch_job_rules: 'auto'
+    allow_path_paste: true
+    expose_user_name: true
+    expose_dataset_path: true
+    expose_potentially_sensitive_job_metrics: true
     require_login: true
-    shed_data_manager_config_file: /home/galaxy/galaxy/config/shed_data_manager_conf.xml
-    shed_tool_config_file: /home/galaxy/galaxy/config/shed_tool_conf.xml
-    shed_tool_data_table_config: /home/galaxy/galaxy/config/shed_tool_data_table_conf.xml
-    smtp_password: !vault |
-          $ANSIBLE_VAULT;1.1;AES256
-          66613031386130396336353334633034653037653336633937386363386233656162396135343663
-          6330363437613665383432626539303330333734633636370a363634353439643030383035636364
-          39393036316235653239633839333032306537356535633334613931343036346461656165616434
-          6330646264373937310a306164643834633230333739643932643961666163313066373162346535
-          35303831363863616134636639306136303934376566383436353833333930383732
-    smtp_server: 'smtp.gmail.com:587'
-    smtp_username: !vault |
-          $ANSIBLE_VAULT;1.1;AES256
-          37616437306334383436313638346266303234646532313263393764393233613361656635616261
-          3336326132616166313134343336303033623966646333370a363135323331353234316431333334
-          33356432346431656636623765363534326237363239643164373830343535346533366331663731
-          6431323561643936330a333939333931633831326133303236353136623138373832383236656462
-          37656139313564376430316133306431313662623463383161376262356263633736
+    # Debugging
+    cleanup_job: onsuccess
+    # Tool security
+    outputs_to_working_directory: true
+    new_user_dataset_access_role_default_private: true # Make datasets private by default
+    # Miscellaneous
+    ftp_upload_dir: /home/galaxy/galaxy/database/ftp
+    ftp_upload_site: ftp://134.157.183.195
+    integrated_tool_panel_config: /home/galaxy/galaxy/config/integrated_tool_panel.xml
+    len_file_path: /home/galaxy/galaxy/config/len
     static_enabled: false
-    tool_config_file: /home/galaxy/galaxy/config/tool_conf.xml
-    tool_data_path: "{{ galaxy_server_dir }}/tool-data"
+    tool_config_file: /home/galaxy/galaxy/config/tool_conf.xml.sample
     tool_data_table_config_path: /home/galaxy/galaxy/config/tool_data_table_conf.xml.sample
-    tool_dependency_dir: /home/galaxy/tool_dependencies
     tool_sheds_config_file: /home/galaxy/galaxy/config/tool_sheds_conf.xml
-    ucsc_build_sites: /home/galaxy/galaxy/tool-data/shared/ucsc/ucsc_build_sites.txt.sample
-    visualization_plugins_directory: config/plugins/visualizations
-    watch_tool_data_dir: true
 
   gravity:
+    process_manager: systemd
     galaxy_root: "{{ galaxy_server_dir }}"
-    app_server: gunicorn
+    galaxy_user: "{{ galaxy_user_name }}"
+    virtualenv: "{{ galaxy_venv_dir }}"
     gunicorn:
       # listening options
       bind: "unix:{{ galaxy_config_dir }}/gunicorn.sock"
@@ -134,7 +135,7 @@ galaxy_config:
 
 # deploy galaxy configuration files
 galaxy_config_files:
-  - src: environments/Conect/files/galaxy/config/job_conf.xml
+  - src: environments/Conect/files/galaxy/config/job_conf.yml
     dest: "{{ galaxy_config.galaxy.job_config_file }}"
   - src: environments/Conect/files/galaxy/config/tool_sheds_conf.xml
     dest: "{{ galaxy_config_dir }}/tool_sheds_conf.xml"
diff --git a/environments/Conect/group_vars/all/nginx b/environments/Conect/group_vars/all/nginx
index 0311f38..0704336 100644
--- a/environments/Conect/group_vars/all/nginx
+++ b/environments/Conect/group_vars/all/nginx
@@ -1,6 +1,7 @@
 ---
 # NGINX
 nginx_server_src_dir: environments/Conect/templates/nginx/
+nginx_selinux_allow_local_connections: true
 nginx_ssl_servers:
   - galaxy
 nginx_enable_default_server: false
diff --git a/environments/Conect/group_vars/all/slurm b/environments/Conect/group_vars/all/slurm
index fa99095..58040fc 100644
--- a/environments/Conect/group_vars/all/slurm
+++ b/environments/Conect/group_vars/all/slurm
@@ -11,3 +11,14 @@ slurm_config:
   SelectType: select/cons_res
   SelectTypeParameters: CR_Core_Memory
 
+slurm_nodes:
+  - name: "localhost"
+    CPUs: 80
+    RealMemory: 385639
+
+slurm_partitions:
+  - name: debug
+    Default: YES
+    DefMemPerCPU: 4820
+    Nodes: "localhost"
+
diff --git a/environments/Conect/group_vars/dbservers.yml b/environments/Conect/group_vars/dbservers.yml
new file mode 120000
index 0000000..2ef78cc
--- /dev/null
+++ b/environments/Conect/group_vars/dbservers.yml
@@ -0,0 +1 @@
+../../dbservers.yml
\ No newline at end of file
diff --git a/environments/Conect/hosts b/environments/Conect/hosts
index 3e18fb5..2a66f3f 100644
--- a/environments/Conect/hosts
+++ b/environments/Conect/hosts
@@ -1,3 +1,6 @@
 [Conect]
-
 localhost  ansible_connection=local ansible_user=root
+
+[dbservers:children]
+Conect
+
diff --git a/environments/Conect/templates/nginx/galaxy.j2 b/environments/Conect/templates/nginx/galaxy.j2
index 69d5dd9..4b7ecff 100644
--- a/environments/Conect/templates/nginx/galaxy.j2
+++ b/environments/Conect/templates/nginx/galaxy.j2
@@ -12,6 +12,10 @@ server {
     # The virtualhost is our domain name
     server_name   "{{ inventory_hostname }}";
 
+    proxy_read_timeout 300;
+    proxy_connect_timeout 300;
+    proxy_send_timeout 300; 
+
     # Our log files will go here.
     access_log /var/log/nginx/access.log;
     error_log /var/log/nginx/error.log;
diff --git a/environments/Docker/group_vars/all/galaxy b/environments/Docker/group_vars/all/galaxy
index cac08a9..e26be76 100644
--- a/environments/Docker/group_vars/all/galaxy
+++ b/environments/Docker/group_vars/all/galaxy
@@ -1,43 +1,63 @@
 ---
 # Docker specific settings
-install_postgresql: no
 install_slurm: no
-galaxy_manage_systemd: no
 
 # Galaxy
 galaxy_additional_venv_packages: drmaa
 galaxy_create_user: true
 galaxy_separate_privileges: true
-# galaxy_manage_paths: true
 galaxy_privsep_user: "{{ galaxy_user }}"
 galaxy_layout: legacy
+galaxy_root: /home/galaxy
 galaxy_server_dir: "{{ galaxy_root }}/galaxy"
+galaxy_user: {name: galaxy, shell: /bin/bash}
 galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
 galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
 galaxy_config_dir: "{{ galaxy_server_dir }}/config"
 galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
-galaxy_root: /home/galaxy
-galaxy_user: {name: galaxy, shell: /bin/bash}
-galaxy_commit_id: release_22.05
+galaxy_commit_id: release_23.0
 galaxy_force_checkout: true
-# galaxy_tool_dependency_dir: "{{ galaxy_server_dir }}/database/tool_dependencies"
 miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
-miniconda_version: 4.7.12
-miniconda_manage_dependencies: false
+miniconda_version: 23.9
+miniconda_channels: ['conda-forge', 'bioconda', 'defaults']
+
 galaxy_config:
   galaxy:
+    admin_users: admin@example.org,tooladmin@galaxy.org
     brand: "🧬🔬🚀"
     builds_file_path: shared/ucsc/builds.txt
-    admin_users: admin@example.org
+    check_migrate_tools: false
     database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
     display_servers: hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
     file_path: datasets
+    job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
     object_store_store_by: id
     tool_data_path: "{{ galaxy_server_dir }}/tool-data"
-    job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
+    # SQL Performance
+    slow_query_log_threshold: 5
+    enable_per_request_sql_debugging: true
+    # File serving perfomance
+    nginx_x_accel_redirect_base: /_x_accel_redirect
+    # Automation / Ease of Use / User-facing features
+    watch_job_rules: 'auto'
+    allow_path_paste: true
+    enable_quotas: true
+    allow_user_deletion: true
+    show_welcome_with_login: true
+    expose_user_name: true
+    expose_dataset_path: true
+    expose_potentially_sensitive_job_metrics: true
+    # Debugging
+    cleanup_job: onsuccess
+    allow_user_impersonation: true
+    # Tool security
+    outputs_to_working_directory: true
+    new_user_dataset_access_role_default_private: true # Make datasets private by default
   gravity:
+    process_manager: systemd
     galaxy_root: "{{ galaxy_server_dir }}"
-    app_server: gunicorn
+    galaxy_user: "{{ galaxy_user_name }}"
+    virtualenv: "{{ galaxy_venv_dir }}"
     gunicorn:
       # listening options
       bind: "unix:{{ galaxy_config_dir }}/gunicorn.sock"
@@ -45,20 +65,22 @@ galaxy_config:
       workers: 2
       # Other options that will be passed to gunicorn
       extra_args: '--forwarded-allow-ips="*"'
+      # This lets Gunicorn start Galaxy completely before forking which is faster.
+      # https://docs.gunicorn.org/en/stable/settings.html#preload-app
       preload: true
     celery:
       concurrency: 2
       loglevel: DEBUG
     handlers:
       handler:
-        processes: 3
+        processes: 2
         pools:
           - job-handler
           - workflow-scheduler
 
 # deploy galaxy configuration files
 galaxy_config_templates:
-  - src: environments/Docker/templates/galaxy/config/job_conf.xml.j2
+  - src: environments/Docker/templates/galaxy/config/job_conf.yml.j2
     dest: "{{ galaxy_config.galaxy.job_config_file }}"
   - src: environments/Docker/templates/galaxy/html/galaxyXpand_welcome.html.j2
     dest: "{{ galaxy_server_dir }}/static/galaxy_welcome.html"
diff --git a/environments/Docker/hosts b/environments/Docker/hosts
index aa2392f..245a916 100644
--- a/environments/Docker/hosts
+++ b/environments/Docker/hosts
@@ -1,3 +1,5 @@
 [Docker]
-
 localhost  ansible_connection=local ansible_user=root
+
+#[dbservers:children]
+#Docker
diff --git a/environments/Docker/templates/galaxy/config/job_conf.xml.j2 b/environments/Docker/templates/galaxy/config/job_conf.xml.j2
deleted file mode 100644
index 16c06a3..0000000
--- a/environments/Docker/templates/galaxy/config/job_conf.xml.j2
+++ /dev/null
@@ -1,44 +0,0 @@
-<job_conf>
-    <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
-    </plugins>
-    <destinations default="local">
-        <destination id="local" runner="local"/>
-        <destination id="gce_multicore" runner="local">
-            <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
-        </destination>
-        <destination id="bowtie" runner="local">
-             <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
-        </destination>
-    </destinations>
-
-    <limits>
-        <limit type="anonymous_user_concurrent_jobs">1</limit>
-        <limit type="registered_user_concurrent_jobs">3</limit>
-        <limit type="destination_user_concurrent_jobs" id="bowtie">1</limit>
-    </limits>
-
-   <tools>
-        <tool id="sam_to_bam" destination="gce_multicore"/>
-        <tool id="sambamba_sample_or_filter" destination="gce_multicore"/>
-        <tool id="bowtie" destination="bowtie"/>
-        <tool id="bowtie_wrapper" destination="bowtie"/>
-        <tool id="bowtie2" destination="bowtie"/>
-        <tool id="bowtieForSmallRNA" destination="bowtie"/>
-        <tool id="bowtie_wrapper" destination="gce_multicore"/>
-        <tool id="mircounts" destination="gce_multicore"/>
-        <tool id="picard_SamToFastq" destination="gce_multicore" />
-        <tool id="rna_star" destination="gce_multicore"/>
-        <tool id="rna_starsolo" destination="gce_multicore"/>
-        <tool id="samtools_cram_to_bam" destination="gce_multicore"/>
-        <tool id="samtools_slice_bam" destination="gce_multicore"/>
-        <tool id="samtools_view" destination="gce_multicore"/>
-        <tool id="samtools_rmdup" destination="gce_multicore"/>
-        <tool id="samtools_fastx" destination="gce_multicore"/>
-        <tool id="samtool_filter2" destination="gce_multicore"/>
-        <tool id="small_rna_maps" destination="gce_multicore"/>
-        <tool id="sr_bowtie_dataset_annotation" destination="bowtie"/>
-        <tool id="bowtie_index_builder_data_manager" destination="gce_multicore"/>
-   </tools>
-
-</job_conf>
diff --git a/environments/Docker/templates/galaxy/config/job_conf.yml.j2 b/environments/Docker/templates/galaxy/config/job_conf.yml.j2
new file mode 100644
index 0000000..666f73e
--- /dev/null
+++ b/environments/Docker/templates/galaxy/config/job_conf.yml.j2
@@ -0,0 +1,45 @@
+# This file is managed by Ansible.
+# Do not edit this file manually. Any changes will be automatically reverted.
+
+runners:
+  local_runner:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 2
+
+handling:
+  assign:
+    - db-skip-locked
+  processes:
+    handler0:
+    handler1:
+
+execution:
+  default: local_env
+  environments:
+    local_env:
+      runner: local_runner
+      tmp_dir: true
+
+    gce_multicore:
+      runner: local_runner
+      local_slots: 2
+      embed_metadata_in_job: true
+    bowtie:
+      runner: local_runner
+      local_slots: 2
+
+limits:
+  - type: anonymous_user_concurrent_jobs
+    value: '1'
+  - type: registered_user_concurrent_jobs
+    value: '3'
+  - type: destination_user_concurrent_jobs
+    id: bowtie
+    value: '1'
+
+tools:
+  - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
+    environment: local_env
+
+  - id: "bowtie_index_builder_data_manager"
+    destination: "gce_multicore"
diff --git a/environments/Docker/templates/nginx/galaxy.j2 b/environments/Docker/templates/nginx/galaxy.j2
index 663bf0d..466dd51 100644
--- a/environments/Docker/templates/nginx/galaxy.j2
+++ b/environments/Docker/templates/nginx/galaxy.j2
@@ -1,9 +1,5 @@
 upstream galaxy {
     server unix:{{ galaxy_mutable_config_dir }}/gunicorn.sock;
-
-    # Or if you serve galaxy at a path like http(s)://fqdn/galaxy
-    # Remember to set galaxy_url_prefix in the galaxy.yml file.
-    # server unix:{{ galaxy_mutable_config_dir }}/gunicorn.sock:/galaxy;
 }
 
 server {
@@ -11,23 +7,19 @@ server {
     listen        *:80 default_server;
     # The virtualhost is our domain name
     server_name   "{{ inventory_hostname }}";
-
     # Our log files will go here.
-    access_log  syslog:server=unix:/dev/log;
-    error_log   syslog:server=unix:/dev/log;
-
+    access_log /var/log/nginx/access.log;
+    error_log /var/log/nginx/error.log;
     # The most important location block, by default all requests are sent to gunicorn
     # If you serve galaxy at a path like /galaxy, change that below (and all other locations!)
     location / {
         # This is the backend to send the requests to.
         proxy_pass http://galaxy;
-
         proxy_set_header Host $http_host;
         proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
         proxy_set_header X-Forwarded-Proto $scheme;
         proxy_set_header Upgrade $http_upgrade;
     }
-
     # Static files can be more efficiently served by Nginx. Why send the
     # request to Gunicorn which should be spending its time doing more useful
     # things like serving Galaxy!
@@ -35,7 +27,6 @@ server {
         alias {{ galaxy_server_dir }}/static;
         expires 24h;
     }
-
     # In Galaxy instances started with run.sh, many config files are
     # automatically copied around. The welcome page is one of them. In
     # production, this step is skipped, so we will manually alias that.
@@ -43,31 +34,24 @@ server {
         alias {{ galaxy_server_dir }}/static/galaxy_welcome.html;
         expires 24h;
     }
-
     # serve visualization and interactive environment plugin static content
     location ~ ^/plugins/(?<plug_type>[^/]+?)/((?<vis_d>[^/_]*)_?)?(?<vis_name>[^/]*?)/static/(?<static_file>.*?)$ {
         alias {{ galaxy_server_dir }}/config/plugins/$plug_type/;
         try_files $vis_d/${vis_d}_${vis_name}/static/$static_file
                   $vis_d/static/$static_file =404;
     }
-
     location /robots.txt {
         alias {{ galaxy_server_dir }}/static/robots.txt;
     }
-
     location /favicon.ico {
         alias {{ galaxy_server_dir }}/static/favicon.ico;
     }
-
     location /_x_accel_redirect {
         internal;
         alias /;
     }
-
     # Support click-to-run in the GTN-in-Galaxy Webhook
     location /training-material/ {
         proxy_pass https://training.galaxyproject.org/training-material/;
     }
-
 }
-
diff --git a/environments/Mississippi/files/galaxy/config/job_conf.xml b/environments/Mississippi/files/galaxy/config/job_conf.xml
deleted file mode 100644
index 83531e3..0000000
--- a/environments/Mississippi/files/galaxy/config/job_conf.xml
+++ /dev/null
@@ -1,113 +0,0 @@
-<?xml version="1.0"?>
-<!-- Do not modify this file, it will we overwritten by ansible galaxykickstart -->
-<job_conf>
-    <plugins workers="4">
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
-        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
-            <param id="drmaa_library_path">/usr/lib/slurm-drmaa/lib/libdrmaa.so</param>
-        </plugin>
-    </plugins>
-
-    <handlers assign_with="db-skip-locked" default="handlers">
-        <handler id="handler_0" tags="handlers"/>
-        <handler id="handler_1" tags="handlers"/>
-        <handler id="handler_2" tags="handlers"/>
-        <handler id="handler_3" tags="handlers"/>
-    </handlers>
-
-    <destinations default="single">
-        <destination id="local" runner="local"/>
-        <destination id="local_multicore" runner="local">
-            <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
-        </destination>
-        <destination id="single" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=1 --share</param>
-        </destination>
-        <destination id="double" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=2 --share</param>
-        </destination>
-        <destination id="four" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=4 --share</param>
-        </destination>
-        <destination id="eight" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate"/>
-            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
-            <param id="nativeSpecification">--ntasks=8 --share</param>
-        </destination>
-    </destinations>
-    <limits>
-        <limit type="anonymous_user_concurrent_jobs">1</limit>
-        <limit type="destination_user_concurrent_jobs" id="single">40</limit>
-        <limit type="destination_user_concurrent_jobs" id="double">20</limit>
-        <limit type="destination_user_concurrent_jobs" id="four">8</limit>
-        <limit type="destination_user_concurrent_jobs" id="eight">6</limit>
-
-        <limit type="destination_total_concurrent_jobs" id="single">40</limit>
-        <limit type="destination_total_concurrent_jobs" id="double">20</limit>
-        <limit type="destination_total_concurrent_jobs" id="four">16</limit>
-        <limit type="destination_total_concurrent_jobs" id="eight">10</limit>
-    </limits>
-   <tools>
-        <tool id="sambamba_filter" destination="single"/>
-        <tool id="sambamba_sample_or_filter" destination="eight"/>
-        <tool id="retrieve_fasta_from_NCBI" destination="double"/>
-        <tool id="picard_MergeSamFiles" destination="eight"/>
-        <tool id="rsembowtie" destination="eight"/>
-        <tool id="rsembowtie2" destination="eight"/>
-        <tool id="tp_grep_tool" destination="single"/>
-        <tool id="circgraph" destination="double"/>
-        <tool id="deeptools_bam_coverage" destination="eight"/>
-        <tool id="deeptools_multi_bam_summary" destination="eight"/>
-        <tool id="deeptools_multi_bigwig_summary" destination="eight"/>
-        <tool id="deeptools_compute_gc_bias" destination="eight"/>
-        <tool id="deeptools_bam_compare" destination="eight"/>
-        <tool id="deeptools_compute_matrix" destination="eight"/>
-        <tool id="deeptools_bigwig_compare" destination="eight"/>
-        <tool id="deeptools_plot_coverage" destination="eight"/>
-        <tool id="tophat2" destination="eight"/>
-        <tool id="hisat2" destination="eight"/>
-        <tool id="bowtie2" destination="eight"/>
-        <tool id="macs2_callpeak" destination="eight"/>
-        <tool id="bowtieForSmallRNA" destination="eight"/>
-        <tool id="bowtie-align" destination="eight"/>
-        <tool id="dexseq" destination="single"/>
-        <tool id="trinity" destination="eight"/>
-        <tool id="oases" destination="eight"/>
-        <tool id="rnaspades" destination="eight"/>
-        <tool id="metaspades" destination="eight"/>
-        <tool id="megahit" destination="eight"/>
-        <tool id="spades" destination="eight"/>
-        <tool id="rna_star" destination="eight"/>
-        <tool id="rgrnastar" destination="eight"/>
-        <tool id="picard_SortSam" destination="eight"/>
-        <tool id="ncbi_blastn_wrapper" destination="eight"/>
-        <tool id="ncbi_blastx_wrapper" destination="eight"/>
-        <tool id="ncbi_tblastx_wrapper" destination="eight"/>
-        <tool id="ncbi_tblastn_wrapper" destination="eight"/>
-        <tool id="abyss-pe" destination="eight"/>
-        <tool id="oaseoptimiserv" destination="eight"/>
-        <tool id="cuffdiff" destination="eight"/>
-        <tool id="run_TEMP" destination="eight"/>
-        <tool id="bwa_mem" destination="eight"/>
-        <tool id="bwa" destination="eight"/>
-        <tool id="breakdancer_max" destination="eight"/>
-        <tool id="salmon" destination="eight"/>
-        <tool id="sr_bowtie_dataset_annotation" destination="eight"/>
-        <tool id="sr_bowtie" destination="eight"/>
-        <tool id="bowtieForSmallRNA" destination="eight"/>
-        <tool id="bowtie" destination="eight"/>
-        <tool id="ngsplot" destination="eight" />
-        <tool id="repenrich" destination="eight"/>
-        <tool id="mircounts" destination="eight"/>
-        <tool id="hicexplorer_hicmergematrixbins" destination="eight"/>
-        <tool id="freebayes" destination="eight"/>
-        <tool id="lofreq_call" destination="eight"/>
-        <tool id="samtools_view" destination="four"/>
-   </tools>
-</job_conf>
diff --git a/environments/Mississippi/files/galaxy/config/job_conf.yml b/environments/Mississippi/files/galaxy/config/job_conf.yml
new file mode 100644
index 0000000..0ac651c
--- /dev/null
+++ b/environments/Mississippi/files/galaxy/config/job_conf.yml
@@ -0,0 +1,243 @@
+# This file is managed by Ansible.
+# Do not edit this file manually. Any changes will be automatically reverted.
+
+runners:
+  local_runner:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 8
+  slurm:
+    load: galaxy.jobs.runners.slurm:SlurmJobRunner
+    drmaa_library_path: /usr/lib/slurm-drmaa/lib/libdrmaa.so
+
+handling:
+  assign:
+    - db-skip-locked
+  processes:
+    handler0:
+    handler1:
+    handler2:
+    handler3:
+
+execution:
+  default: cluster_1
+  environments:
+    local_env:
+      runner: local_runner
+      tmp_dir: true
+    gce_multicore:
+      runner: local_runner
+      local_slots: 2
+      embed_metadata_in_job: true
+    cluster_1:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=1"
+    cluster_2:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=2"
+    cluster_4:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=4"
+    cluster_8:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=8"
+
+limits:
+  - type: anonymous_user_concurrent_jobs
+    value: '1'
+  - type: registered_user_concurrent_jobs
+    value: '10'
+
+  - type: environment_total_concurrent_jobs
+    id: cluster_1
+    value: 70
+  - type: environment_total_concurrent_jobs
+    id: cluster_2
+    value: 35
+  - type: environment_total_concurrent_jobs
+    id: cluster_4
+    value: 18
+  - type: environment_total_concurrent_jobs
+    id: cluster_8
+    value: 10
+
+  - type: environment_user_concurrent_jobs
+    id: cluster_1
+    value: 50
+  - type: environment_user_concurrent_jobs
+    id: cluster_2
+    value: 25
+  - type: environment_user_concurrent_jobs
+    id: cluster_4
+    value: 15
+  - type: environment_user_concurrent_jobs
+    id: cluster_8
+    value: 8
+
+tools:
+  - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
+    environment: local_env
+
+  - id: "abyss-pe"
+    destination: "cluster_8"
+
+  - id: "bowtie_wrapper"
+    destination: "cluster_8"
+
+  - id: "bowtie2"
+    destination: "cluster_8"
+
+  - id: "bowtieForSmallRNA"
+    destination: "cluster_8"
+
+  - id: "breakdancer_max"
+    destination: "cluster_8"
+
+  - id: "bwa"
+    destination: "cluster_8"
+
+  - id: "bwa_mem"
+    destination: "cluster_8"
+
+  - id: "circgraph"
+    destination: "cluster_2"
+
+  - id: "cuffdiff"
+    destination: "cluster_8"
+
+  - id: "deeptools_bam_compare"
+    destination: "cluster_8"
+
+  - id: "deeptools_bam_coverage"
+    destination: "cluster_8"
+
+  - id: "deeptools_bigwig_compare"
+    destination: "cluster_8"
+
+  - id: "deeptools_compute_gc_bias"
+    destination: "cluster_8"
+
+  - id: "deeptools_compute_matrix"
+    destination: "cluster_8"
+
+  - id: "deeptools_multi_bam_summary"
+    destination: "cluster_8"
+
+  - id: "deeptools_multi_bigwig_summary"
+    destination: "cluster_8"
+
+  - id: "deeptools_plot_coverage"
+    destination: "cluster_8"
+
+  - id: "dexseq"
+    destination: "cluster_1"
+
+  - id: "fastqc"
+    destination: "cluster_8"
+
+  - id: "freebayes"
+    destination: "cluster_8"
+
+  - id: "hicexplorer_hicmergematrixbins"
+    destination: "cluster_8"
+
+  - id: "hisat2"
+    destination: "cluster_8"
+
+  - id: "lofreq_call"
+    destination: "cluster_8"
+
+  - id: "macs2_callpeak"
+    destination: "cluster_8"
+
+  - id: "megahit"
+    destination: "cluster_8"
+
+  - id: "metaspades"
+    destination: "cluster_8"
+
+  - id: "mircounts"
+    destination: "cluster_8"
+
+  - id: "ncbi_blastn_wrapper"
+    destination: "cluster_8"
+
+  - id: "ncbi_blastx_wrapper"
+    destination: "cluster_8"
+
+  - id: "ncbi_tblastn_wrapper"
+    destination: "cluster_8"
+
+  - id: "ncbi_tblastx_wrapper"
+    destination: "cluster_8"
+
+  - id: "ngsplot"
+    destination: "cluster_8"
+
+  - id: "oaseoptimiserv"
+    destination: "cluster_8"
+
+  - id: "oases"
+    destination: "cluster_8"
+
+  - id: "picard_MergeSamFiles"
+    destination: "cluster_8"
+
+  - id: "picard_SortSam"
+    destination: "cluster_8"
+
+  - id: "repenrich"
+    destination: "cluster_8"
+
+  - id: "retrieve_fasta_from_NCBI"
+    destination: "cluster_2"
+
+  - id: "rgrnastar"
+    destination: "cluster_8"
+
+  - id: "rna_star"
+    destination: "cluster_8"
+
+  - id: "rnaspades"
+    destination: "cluster_8"
+
+  - id: "rsembowtie"
+    destination: "cluster_8"
+
+  - id: "rsembowtie2"
+    destination: "cluster_8"
+
+  - id: "run_TEMP"
+    destination: "cluster_8"
+
+  - id: "salmon"
+    destination: "cluster_8"
+
+  - id: "sambamba_filter"
+    destination: "cluster_1"
+
+  - id: "sambamba_sample_or_filter"
+    destination: "cluster_8"
+
+  - id: "samtools_view"
+    destination: "cluster_4"
+
+  - id: "spades"
+    destination: "cluster_8"
+
+  - id: "sr_bowtie"
+    destination: "cluster_8"
+
+  - id: "sr_bowtie_dataset_annotation"
+    destination: "cluster_8"
+
+  - id: "tophat2"
+    destination: "cluster_8"
+
+  - id: "tp_grep_tool"
+    destination: "cluster_1"
+
+  - id: "trinity"
+    destination: "cluster_8"
+
+  - id: "yac"
+    destination: "cluster_1"
diff --git a/environments/Mississippi/files/galaxy/config/mississippi_tool_list.yml b/environments/Mississippi/files/galaxy/config/mississippi_tool_list.yml
index 5850e2e..c581861 100644
--- a/environments/Mississippi/files/galaxy/config/mississippi_tool_list.yml
+++ b/environments/Mississippi/files/galaxy/config/mississippi_tool_list.yml
@@ -49,6 +49,11 @@ tools:
   tool_panel_section_id: collection_operations
   tool_panel_section_label: Collection Operations
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: add_column_headers
+  owner: estrain
+  tool_panel_section_id: textutil
+  tool_panel_section_label: Text Manipulation
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: csv_to_tabular
   owner: mnhn65mo
   tool_panel_section_id: textutil
@@ -134,6 +139,21 @@ tools:
   tool_panel_section_id: textutil
   tool_panel_section_label: Text Manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: annotatemyids
+  owner: iuc
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: gtftobed12
+  owner: iuc
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: fastq_groomer
+  owner: devteam
+  tool_panel_section_id: convert
+  tool_panel_section_label: Convert Formats
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: crossmap_wig
   owner: iuc
   tool_panel_section_id: convert
@@ -169,11 +189,6 @@ tools:
   tool_panel_section_id: convert
   tool_panel_section_label: Convert Formats
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gtftobed12
-  owner: iuc
-  tool_panel_section_id: convert
-  tool_panel_section_label: Convert Formats
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: genbank_to_fasta
   owner: portiahollyoak
   tool_panel_section_id: convert
@@ -274,6 +289,11 @@ tools:
   tool_panel_section_id: bxops
   tool_panel_section_label: Operate on Genomic Intervals
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: compute_wilcoxon_test
+  owner: bebatut
+  tool_panel_section_id: stats
+  tool_panel_section_label: Statistics
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: heat_map_creation
   owner: md-anderson-bioinformatics
   tool_panel_section_id: stats
@@ -359,6 +379,16 @@ tools:
   tool_panel_section_id: plots
   tool_panel_section_label: Graph/Display Data
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: deeptools_bam_coverage
+  owner: bgruening
+  tool_panel_section_id: deeptools
+  tool_panel_section_label: DeepTools
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: deeptools_compute_matrix
+  owner: bgruening
+  tool_panel_section_id: deeptools
+  tool_panel_section_label: DeepTools
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: deeptools_plot_coverage
   owner: bgruening
   tool_panel_section_id: deeptools
@@ -404,11 +434,6 @@ tools:
   tool_panel_section_id: deeptools
   tool_panel_section_label: DeepTools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deeptools_compute_matrix
-  owner: bgruening
-  tool_panel_section_id: deeptools
-  tool_panel_section_label: DeepTools
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: deeptools_plot_profile
   owner: bgruening
   tool_panel_section_id: deeptools
@@ -419,11 +444,6 @@ tools:
   tool_panel_section_id: deeptools
   tool_panel_section_label: DeepTools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deeptools_bam_coverage
-  owner: bgruening
-  tool_panel_section_id: deeptools
-  tool_panel_section_label: DeepTools
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: deeptools_compute_matrix_operations
   owner: bgruening
   tool_panel_section_id: deeptools
@@ -454,18 +474,18 @@ tools:
   tool_panel_section_id: deeptools
   tool_panel_section_label: DeepTools
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: fetch_fasta_from_ncbi
+- name: blastparser_and_hits
   owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: ncbi_blast_plus
-  owner: devteam
+- name: fetch_fasta_from_ncbi
+  owner: artbio
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blastparser_and_hits
-  owner: artbio
+- name: ncbi_blast_plus
+  owner: devteam
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -494,11 +514,6 @@ tools:
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: regex_find_replace
-  owner: galaxyp
-  tool_panel_section_id: metavisitor
-  tool_panel_section_label: Metavisitor
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: reverse_complement
   owner: xuebing
   tool_panel_section_id: metavisitor
@@ -509,8 +524,8 @@ tools:
   tool_panel_section_id: metavisitor
   tool_panel_section_label: Metavisitor
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: trinity_analyze_diff_expr
-  owner: iuc
+- name: cpm_tpm_rpk
+  owner: artbio
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -519,6 +534,16 @@ tools:
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: deseq2
+  owner: iuc
+  tool_panel_section_id: differential_expression
+  tool_panel_section_label: Differential Expression
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: trinity_analyze_diff_expr
+  owner: iuc
+  tool_panel_section_id: differential_expression
+  tool_panel_section_label: Differential Expression
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: volcanoplot
   owner: iuc
   tool_panel_section_id: differential_expression
@@ -539,11 +564,6 @@ tools:
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: deseq2
-  owner: iuc
-  tool_panel_section_id: differential_expression
-  tool_panel_section_label: Differential Expression
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: featurecounts
   owner: iuc
   tool_panel_section_id: differential_expression
@@ -564,16 +584,16 @@ tools:
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: cpm_tpm_rpk
-  owner: artbio
-  tool_panel_section_id: differential_expression
-  tool_panel_section_label: Differential Expression
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: ruvseq
   owner: iuc
   tool_panel_section_id: differential_expression
   tool_panel_section_label: Differential Expression
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: artbio_bam_cleaning
+  owner: artbio
+  tool_panel_section_id: ngs:_qc_and_manipulation
+  tool_panel_section_label: 'NGS: QC and manipulation'
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: khmer_normalize_by_median
   owner: iuc
   tool_panel_section_id: ngs:_qc_and_manipulation
@@ -629,11 +649,6 @@ tools:
   tool_panel_section_id: ngs:_qc_and_manipulation
   tool_panel_section_label: 'NGS: QC and manipulation'
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sample
-  owner: cjav
-  tool_panel_section_id: ngs:_qc_and_manipulation
-  tool_panel_section_label: 'NGS: QC and manipulation'
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: fasta_clipping_histogram
   owner: devteam
   tool_panel_section_id: ngs:_qc_and_manipulation
@@ -904,18 +919,18 @@ tools:
   tool_panel_section_id: fasta_manipulation
   tool_panel_section_label: FASTA manipulation
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: breseq
-  owner: iuc
+- name: lumpy_smoove
+  owner: artbio
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: gatk4_mutect2
+- name: breseq
   owner: iuc
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: lumpy_smoove
-  owner: artbio
+- name: gatk4_mutect2
+  owner: iuc
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
@@ -1004,22 +1019,22 @@ tools:
   tool_panel_section_id: genomic_variants
   tool_panel_section_label: Genomic Variants
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: yac_clipper
+- name: small_rna_signatures
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sr_bowtie_dataset_annotation
+- name: yac_clipper
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sr_bowtie
+- name: sr_bowtie_dataset_annotation
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: small_rna_signatures
+- name: sr_bowtie
   owner: artbio
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
@@ -1054,11 +1069,6 @@ tools:
   tool_panel_section_id: mississippi_tool_suite
   tool_panel_section_label: Mississippi Tool Suite
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: bamparse
-  owner: artbio
-  tool_panel_section_id: mississippi_tool_suite
-  tool_panel_section_label: Mississippi Tool Suite
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: bowtie2
   owner: devteam
   tool_panel_section_id: ngs:_mapping
@@ -1164,6 +1174,16 @@ tools:
   tool_panel_section_id: bedtools
   tool_panel_section_label: BEDtools
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: bamparse
+  owner: artbio
+  tool_panel_section_id: ngs:_sam_tools
+  tool_panel_section_label: 'NGS: SAM Tools'
+  tool_shed_url: toolshed.g2.bx.psu.edu
+- name: samtools_idxstats
+  owner: devteam
+  tool_panel_section_id: ngs:_sam_tools
+  tool_panel_section_label: 'NGS: SAM Tools'
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: samtool_filter2
   owner: devteam
   tool_panel_section_id: ngs:_sam_tools
@@ -1354,11 +1374,6 @@ tools:
   tool_panel_section_id: metavisitor_2
   tool_panel_section_label: METAVISITOR_2
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: blastparser_and_hits
-  owner: artbio
-  tool_panel_section_id: metavisitor_2
-  tool_panel_section_label: METAVISITOR_2
-  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: blast_unmatched
   owner: artbio
   tool_panel_section_id: metavisitor_2
@@ -1629,3 +1644,8 @@ tools:
   tool_panel_section_id: None
   tool_panel_section_label: None
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: data_manager_hisat2_index_builder
+  owner: iuc
+  tool_panel_section_id: None
+  tool_panel_section_label: None
+  tool_shed_url: toolshed.g2.bx.psu.edu
diff --git a/environments/Mississippi/files/galaxy/html/welcome.html b/environments/Mississippi/files/galaxy/html/welcome.html
index 05e8b8c..1a03959 100644
--- a/environments/Mississippi/files/galaxy/html/welcome.html
+++ b/environments/Mississippi/files/galaxy/html/welcome.html
@@ -25,19 +25,19 @@
 
         <div class="alert alert-success" style="margin-top: 0.5em">
         <div>
-               <p><h3>
-                  Error reporting using automated emails has been fixed.
-                  You can report your mistakes and encountered bugs again!
-               </h3></p>
+               <p><h3><center>
+                  Welcome to Mississippi[2] server
+               </center></h3></p>
                <p>Mississippi[2] is deployed using
                   <a href="/ARTbio/galaxyXpand" target="_blank"> galaxyXpand.</a>
+                  and was upgraded to release_23.0 version on January 5th, 2024.
                </p>
                <p>Users may request tool installation by raising a pull request after editing the
                   <a href="/ARTbio/galaxyXpand/blob/main/environments/Mississippi/files/galaxy/config/mississippi_tool_list.yml" target="_blank">
                   mississippi_tool_list.yml </a> on our <a href="/ARTbio/galaxyXpand" target="_blank"> GitHub galaxyXpand </a> repository.
                </p>
         </div>
-	
+
         </div>
 
         <!-- -->
diff --git a/environments/Mississippi/group_vars/all/galaxy b/environments/Mississippi/group_vars/all/galaxy
index 606ba49..1e03721 100644
--- a/environments/Mississippi/group_vars/all/galaxy
+++ b/environments/Mississippi/group_vars/all/galaxy
@@ -1,29 +1,29 @@
 ---
 # Galaxy
 galaxy_additional_venv_packages: drmaa
+galaxy_commit_id: release_23.0
+galaxy_config_dir: "{{ galaxy_server_dir }}/config"
+galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
 galaxy_create_user: true
-galaxy_separate_privileges: true
-galaxy_privsep_user: "{{ galaxy_user }}"
+galaxy_force_checkout: true
 galaxy_layout: legacy
-galaxy_server_dir: "{{ galaxy_root }}/galaxy"
-galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
+galaxy_manage_cleanup: yes  # Install a cron job to clean up Galaxy framework and job execution temporary
 galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
-galaxy_config_dir: "{{ galaxy_server_dir }}/config"
-galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
+galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
+galaxy_privsep_user: "{{ galaxy_user }}"
 galaxy_root: /home/galaxy
-galaxy_user: {name: galaxy, shell: /bin/bash}
-galaxy_commit_id: release_22.05
-galaxy_force_checkout: true
+galaxy_separate_privileges: true
+galaxy_server_dir: "{{ galaxy_root }}/galaxy"
 galaxy_tool_dependency_dir: "{{ galaxy_root }}/tool_dependencies"
-galaxy_manage_cleanup: yes  # Install a cron job to clean up Galaxy framework and job execution temporary
+galaxy_user: {name: galaxy, shell: /bin/bash}
+miniconda_channels: ['conda-forge', 'bioconda', 'defaults']
 miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
-miniconda_version: 4.7.12
-miniconda_manage_dependencies: false
+miniconda_version: 23.9
+
 galaxy_config:
   galaxy:
     brand: "🧬 Mississippi[2]"
     builds_file_path: shared/ucsc/builds.txt
-    display_servers: hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
     admin_users: !vault |
           $ANSIBLE_VAULT;1.1;AES256
           39653064333539343430663435376264653839386234306239356664356532633534623364306333
@@ -33,6 +33,7 @@ galaxy_config:
           63316466613366346464316131316663366338386639303537313533656333656637626365323465
           38396235363832343430613230363236383538303066383163306264663961666266366335646336
           663636386537363938666438353139626637
+    display_servers: hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
     smtp_username: !vault |
           $ANSIBLE_VAULT;1.1;AES256
           61613536306433356230663264663932373037316337346561653530333630643933636233396130
@@ -74,16 +75,31 @@ galaxy_config:
           32373437303433353230353030336334353661316537643736383239383036306264653334626435
           6239373664353064613166313031623534313366346230333932
     tool_data_path: "{{ galaxy_server_dir }}/tool-data"
-    job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
-    allow_user_impersonation: true
-    allow_user_dataset_purge: true
-    enable_quotas: true
-    allow_user_deletion: true
+    job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
     allow_library_path_paste: true
     watch_tool_data_dir: true
+    # File serving perfomance
     nginx_x_accel_redirect_base: /_x_accel_redirect
+    # SQL Performance
+    slow_query_log_threshold: 5
+    enable_per_request_sql_debugging: true
+    # Automation / Ease of Use / User-facing features
+    allow_user_dataset_purge: true
+    enable_quotas: true
+    allow_user_deletion: true
+    allow_user_impersonation: true
+    watch_job_rules: 'auto'
+    allow_path_paste: true
+    expose_user_name: true
+    expose_dataset_path: true
     expose_potentially_sensitive_job_metrics: true
     require_login: true
+    # Debugging
+    cleanup_job: onsuccess
+    # Tool security
+    outputs_to_working_directory: true
+    new_user_dataset_access_role_default_private: true # Make datasets private by default
+    # Miscellaneous
     ftp_upload_dir: /home/galaxy/galaxy/database/ftp
     ftp_upload_site: ftp://134.157.183.152
     integrated_tool_panel_config: /home/galaxy/galaxy/config/integrated_tool_panel.xml
@@ -91,12 +107,13 @@ galaxy_config:
     static_enabled: false
     tool_config_file: /home/galaxy/galaxy/config/tool_conf.xml
     tool_data_table_config_path: /home/galaxy/galaxy/config/tool_data_table_conf.xml.sample
-    tool_dependency_dir: /home/galaxy/tool_dependencies
     tool_sheds_config_file: /home/galaxy/galaxy/config/tool_sheds_conf.xml
 
   gravity:
+    process_manager: systemd
     galaxy_root: "{{ galaxy_server_dir }}"
-    app_server: gunicorn
+    galaxy_user: "{{ galaxy_user_name }}"
+    virtualenv: "{{ galaxy_venv_dir }}"
     gunicorn:
       # listening options
       bind: "unix:{{ galaxy_config_dir }}/gunicorn.sock"
@@ -117,7 +134,7 @@ galaxy_config:
 
 # deploy galaxy configuration files
 galaxy_config_files:
-  - src: environments/Mississippi/files/galaxy/config/job_conf.xml
+  - src: environments/Mississippi/files/galaxy/config/job_conf.yml
     dest: "{{ galaxy_config.galaxy.job_config_file }}"
   - src: environments/Mississippi/files/galaxy/config/tool_sheds_conf.xml
     dest: "{{ galaxy_config_dir }}/tool_sheds_conf.xml"
diff --git a/environments/Mississippi/group_vars/all/nginx b/environments/Mississippi/group_vars/all/nginx
index 2f74d08..31e61fa 100644
--- a/environments/Mississippi/group_vars/all/nginx
+++ b/environments/Mississippi/group_vars/all/nginx
@@ -1,6 +1,7 @@
 ---
 # NGINX
 nginx_server_src_dir: environments/Mississippi/templates/nginx/
+nginx_selinux_allow_local_connections: true
 nginx_ssl_servers:
   - galaxy
 nginx_enable_default_server: false
diff --git a/environments/Mississippi/group_vars/all/slurm b/environments/Mississippi/group_vars/all/slurm
index fa99095..c05b043 100644
--- a/environments/Mississippi/group_vars/all/slurm
+++ b/environments/Mississippi/group_vars/all/slurm
@@ -11,3 +11,13 @@ slurm_config:
   SelectType: select/cons_res
   SelectTypeParameters: CR_Core_Memory
 
+slurm_nodes:
+  - name: "localhost"
+    CPUs: 80
+    RealMemory: 385558
+
+slurm_partitions:
+  - name: debug
+    Default: YES
+    DefMemPerCPU: 4819
+    Nodes: "localhost"
diff --git a/environments/Mississippi/group_vars/dbservers.yml b/environments/Mississippi/group_vars/dbservers.yml
new file mode 120000
index 0000000..2ef78cc
--- /dev/null
+++ b/environments/Mississippi/group_vars/dbservers.yml
@@ -0,0 +1 @@
+../../dbservers.yml
\ No newline at end of file
diff --git a/environments/Mississippi/hosts b/environments/Mississippi/hosts
index 662fecb..839b145 100644
--- a/environments/Mississippi/hosts
+++ b/environments/Mississippi/hosts
@@ -1,3 +1,4 @@
 [Mississippi]
-
 localhost  ansible_connection=local ansible_user=root
+[dbservers:children]
+Mississippi
diff --git a/environments/Mississippi/templates/nginx/galaxy.j2 b/environments/Mississippi/templates/nginx/galaxy.j2
index f950470..45273b3 100644
--- a/environments/Mississippi/templates/nginx/galaxy.j2
+++ b/environments/Mississippi/templates/nginx/galaxy.j2
@@ -12,6 +12,10 @@ server {
     # The virtualhost is our domain name
     server_name   "{{ inventory_hostname }}";
 
+    proxy_read_timeout 300;
+    proxy_connect_timeout 300;
+    proxy_send_timeout 300; 
+
     # Our log files will go here.
     access_log /var/log/nginx/access.log;
     error_log /var/log/nginx/error.log;
@@ -69,5 +73,4 @@ server {
         proxy_pass https://training.galaxyproject.org/training-material/;
     }
 
-
 }
diff --git a/environments/dbservers.yml b/environments/dbservers.yml
new file mode 100644
index 0000000..1f74019
--- /dev/null
+++ b/environments/dbservers.yml
@@ -0,0 +1,6 @@
+# PostgreSQL
+postgresql_objects_users:
+  - name: "{{ galaxy_user_name }}"
+postgresql_objects_databases:
+  - name: "{{ galaxy_db_name }}"
+    owner: "{{ galaxy_user_name }}"
diff --git a/environments/dev_gce/group_vars/all/galaxy b/environments/dev_gce/group_vars/all/galaxy
index 1b8367d..1625448 100644
--- a/environments/dev_gce/group_vars/all/galaxy
+++ b/environments/dev_gce/group_vars/all/galaxy
@@ -6,19 +6,19 @@ galaxy_separate_privileges: true
 # galaxy_manage_paths: true
 galaxy_privsep_user: "{{ galaxy_user }}"
 galaxy_layout: legacy
+galaxy_root: /home/galaxy
 galaxy_server_dir: "{{ galaxy_root }}/galaxy"
+galaxy_user: {name: galaxy, shell: /bin/bash}
 galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
 galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
 galaxy_config_dir: "{{ galaxy_server_dir }}/config"
 galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
-galaxy_root: /home/galaxy
-galaxy_user: {name: galaxy, shell: /bin/bash}
-galaxy_commit_id: release_22.05
+galaxy_commit_id: release_23.0
 galaxy_force_checkout: true
-# galaxy_tool_dependency_dir: "{{ galaxy_server_dir }}/database/tool_dependencies"
 miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
-miniconda_version: 4.7.12
-miniconda_manage_dependencies: false
+miniconda_version: 23.9
+miniconda_channels: ['conda-forge', 'defaults']
+
 galaxy_config:
   galaxy:
     admin_users: admin@example.org,tooladmin@galaxy.org
@@ -28,15 +28,34 @@ galaxy_config:
     display_servers: hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
     expose_dataset_path: true
     file_path: datasets
-    job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
+    job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
     object_store_store_by: id
     tool_data_path: "{{ galaxy_server_dir }}/tool-data"
+    # SQL Performance
+    slow_query_log_threshold: 5
+    enable_per_request_sql_debugging: true
+    # File serving perfomance
+    nginx_x_accel_redirect_base: /_x_accel_redirect
+    # Automation / Ease of Use / User-facing features
+    watch_job_rules: 'auto'
+    allow_path_paste: true
+    enable_quotas: true
+    allow_user_deletion: true
+    show_welcome_with_login: true
+    expose_user_name: true
+    expose_dataset_path: true
+    expose_potentially_sensitive_job_metrics: true
+    # Debugging
+    cleanup_job: onsuccess
+    allow_user_impersonation: true
+    # Tool security
+    outputs_to_working_directory: true
+    new_user_dataset_access_role_default_private: true # Make datasets private by default
   gravity:
-    app_server: gunicorn
-    celery:
-      concurrency: 2
-      loglevel: DEBUG
+    process_manager: systemd
     galaxy_root: "{{ galaxy_server_dir }}"
+    galaxy_user: "{{ galaxy_user_name }}"
+    virtualenv: "{{ galaxy_venv_dir }}"
     gunicorn:
       # listening options
       bind: "localhost:4000"
@@ -44,7 +63,12 @@ galaxy_config:
       workers: 2
       # Other options that will be passed to gunicorn
       extra_args: '--forwarded-allow-ips="*"'
+      # This lets Gunicorn start Galaxy completely before forking which is faster.
+      # https://docs.gunicorn.org/en/stable/settings.html#preload-app
       preload: true
+    celery:
+      concurrency: 2
+      loglevel: DEBUG
     handlers:
       handler:
         processes: 2
@@ -54,7 +78,7 @@ galaxy_config:
 
 # deploy galaxy configuration files
 galaxy_config_templates:
-  - src: environments/dev_gce/templates/galaxy/config/job_conf.xml.j2
+  - src: environments/dev_gce/templates/galaxy/config/job_conf.yml.j2
     dest: "{{ galaxy_config.galaxy.job_config_file }}"
   - src: environments/dev_gce/templates/galaxy/html/galaxyXpand_welcome.html.j2
     dest: "{{ galaxy_server_dir }}/static/galaxy_welcome.html"
diff --git a/environments/dev_gce/group_vars/dbservers.yml b/environments/dev_gce/group_vars/dbservers.yml
new file mode 120000
index 0000000..2ef78cc
--- /dev/null
+++ b/environments/dev_gce/group_vars/dbservers.yml
@@ -0,0 +1 @@
+../../dbservers.yml
\ No newline at end of file
diff --git a/environments/dev_gce/hosts b/environments/dev_gce/hosts
index cfb7616..07e53c3 100644
--- a/environments/dev_gce/hosts
+++ b/environments/dev_gce/hosts
@@ -1,3 +1,5 @@
 [dev_gce]
-
 localhost  ansible_connection=local ansible_user=ubuntu
+
+[dbservers:children]
+dev_gce
diff --git a/environments/dev_gce/templates/galaxy/config/job_conf.xml.j2 b/environments/dev_gce/templates/galaxy/config/job_conf.xml.j2
deleted file mode 100644
index 55984b9..0000000
--- a/environments/dev_gce/templates/galaxy/config/job_conf.xml.j2
+++ /dev/null
@@ -1,61 +0,0 @@
-<job_conf>
-    <plugins>
-        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" workers="4">
-            <param id="drmaa_library_path">/usr/lib/slurm-drmaa/lib/libdrmaa.so</param>
-        </plugin>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
-    </plugins>
-
-    <handlers assign_with="db-skip-locked" default="handlers">
-        <handler id="handler_0" tags="handlers"/>
-        <handler id="handler_1" tags="handlers"/>
-    </handlers>
-
-    <destinations default="local">
-        <destination id="local" runner="local"/>
-        <destination id="gce_multicore" runner="local">
-            <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
-        </destination>
-        <destination id="bowtie" runner="local">
-             <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
-        </destination>
-        <destination id="cluster_4" runner="slurm">
-             <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-             <param id="type">python</param>
-             <param id="nativeSpecification">--partition=debug --ntasks=4</param>
-             <param id="docker_sudo">false</param>
-             <param id="docker_volumes_from">galaxy</param>
-        </destination>
-    </destinations>
-
-    <limits>
-        <limit type="anonymous_user_concurrent_jobs">1</limit>
-        <limit type="registered_user_concurrent_jobs">3</limit>
-        <limit type="destination_user_concurrent_jobs" id="bowtie">1</limit>
-    </limits>
-
-   <tools>
-        <tool id="sam_to_bam" destination="gce_multicore"/>
-        <tool id="sambamba_sample_or_filter" destination="gce_multicore"/>
-        <tool id="bowtie" destination="bowtie"/>
-        <tool id="bowtie_wrapper" destination="bowtie"/>
-        <tool id="bowtie2" destination="bowtie"/>
-        <tool id="bowtieForSmallRNA" destination="bowtie"/>
-        <tool id="bowtie_wrapper" destination="gce_multicore"/>
-        <tool id="mircounts" destination="gce_multicore"/>
-        <tool id="picard_SamToFastq" destination="gce_multicore" />
-        <tool id="rna_star" destination="gce_multicore"/>
-        <tool id="rna_starsolo" destination="gce_multicore"/>
-        <tool id="samtools_cram_to_bam" destination="gce_multicore"/>
-        <tool id="samtools_slice_bam" destination="gce_multicore"/>
-        <tool id="samtools_view" destination="gce_multicore"/>
-        <tool id="samtools_rmdup" destination="gce_multicore"/>
-        <tool id="samtools_fastx" destination="gce_multicore"/>
-        <tool id="samtool_filter2" destination="gce_multicore"/>
-        <tool id="small_rna_maps" destination="gce_multicore"/>
-        <tool id="sr_bowtie_dataset_annotation" destination="bowtie"/>
-        <tool id="bowtie_index_builder_data_manager" destination="gce_multicore"/>
-        <tool id="retrieve_fasta_from_NCBI" destination="cluster_4"/>
-   </tools>
-
-</job_conf>
diff --git a/environments/dev_gce/templates/galaxy/config/job_conf.yml.j2 b/environments/dev_gce/templates/galaxy/config/job_conf.yml.j2
new file mode 100644
index 0000000..54429dc
--- /dev/null
+++ b/environments/dev_gce/templates/galaxy/config/job_conf.yml.j2
@@ -0,0 +1,57 @@
+# This file is managed by Ansible.
+# Do not edit this file manually. Any changes will be automatically reverted.
+
+runners:
+  local_runner:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+    workers: 2
+  slurm:
+    load: galaxy.jobs.runners.slurm:SlurmJobRunner
+    drmaa_library_path: /usr/lib/slurm-drmaa/lib/libdrmaa.so
+
+handling:
+  assign:
+    - db-skip-locked
+  processes:
+    handler0:
+    handler1:
+
+execution:
+  default: local_env
+  environments:
+    local_env:
+      runner: local_runner
+      tmp_dir: true
+
+    gce_multicore:
+      runner: local_runner
+      local_slots: 2
+      embed_metadata_in_job: true
+    bowtie:
+      runner: local_runner
+      local_slots: 2
+    cluster:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=1"
+
+limits:
+  - type: anonymous_user_concurrent_jobs
+    value: '1'
+  - type: registered_user_concurrent_jobs
+    value: '3'
+  - type: destination_user_concurrent_jobs
+    id: bowtie
+    value: '1'
+
+tools:
+  - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
+    environment: local_env
+
+  - id: "bowtieForSmallRNA"
+    destination: "cluster"
+
+  - id: "bowtie_index_builder_data_manager"
+    destination: "gce_multicore"
+
+  - id: "retrieve_fasta_from_NCBI"
+    destination: "cluster"
diff --git a/environments/dev_gce/templates/nginx/galaxy.j2 b/environments/dev_gce/templates/nginx/galaxy.j2
index dfba5e0..9849fbd 100644
--- a/environments/dev_gce/templates/nginx/galaxy.j2
+++ b/environments/dev_gce/templates/nginx/galaxy.j2
@@ -11,23 +11,19 @@ server {
     listen        *:80 default_server;
     # The virtualhost is our domain name
     server_name   "{{ inventory_hostname }}";
-
     # Our log files will go here.
     access_log /var/log/nginx/access.log;
     error_log /var/log/nginx/error.log;
-
     # The most important location block, by default all requests are sent to gunicorn
     # If you serve galaxy at a path like /galaxy, change that below (and all other locations!)
     location / {
         # This is the backend to send the requests to.
         proxy_pass http://galaxy;
-
         proxy_set_header Host $http_host;
         proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
         proxy_set_header X-Forwarded-Proto $scheme;
         proxy_set_header Upgrade $http_upgrade;
     }
-
     # Static files can be more efficiently served by Nginx. Why send the
     # request to Gunicorn which should be spending its time doing more useful
     # things like serving Galaxy!
@@ -35,7 +31,6 @@ server {
         alias {{ galaxy_server_dir }}/static;
         expires 24h;
     }
-
     # In Galaxy instances started with run.sh, many config files are
     # automatically copied around. The welcome page is one of them. In
     # production, this step is skipped, so we will manually alias that.
@@ -43,31 +38,24 @@ server {
         alias {{ galaxy_server_dir }}/static/galaxy_welcome.html;
         expires 24h;
     }
-
     # serve visualization and interactive environment plugin static content
     location ~ ^/plugins/(?<plug_type>[^/]+?)/((?<vis_d>[^/_]*)_?)?(?<vis_name>[^/]*?)/static/(?<static_file>.*?)$ {
         alias {{ galaxy_server_dir }}/config/plugins/$plug_type/;
         try_files $vis_d/${vis_d}_${vis_name}/static/$static_file
                   $vis_d/static/$static_file =404;
     }
-
     location /robots.txt {
         alias {{ galaxy_server_dir }}/static/robots.txt;
     }
-
     location /favicon.ico {
         alias {{ galaxy_server_dir }}/static/favicon.ico;
     }
-
     location /_x_accel_redirect {
         internal;
         alias /;
     }
-
     # Support click-to-run in the GTN-in-Galaxy Webhook
     location /training-material/ {
         proxy_pass https://training.galaxyproject.org/training-material/;
     }
-
 }
-
diff --git a/environments/dev_mississippi/files/galaxy/config/job_conf.xml b/environments/dev_mississippi/files/galaxy/config/job_conf.xml
deleted file mode 100644
index 25994e2..0000000
--- a/environments/dev_mississippi/files/galaxy/config/job_conf.xml
+++ /dev/null
@@ -1,89 +0,0 @@
-<?xml version="1.0"?>
-<job_conf>
-    <plugins workers="4">
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
-        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
-            <param id="drmaa_library_path">/usr/lib/slurm-drmaa/lib/libdrmaa.so</param>
-        </plugin>
-    </plugins>
-
-    <handlers assign_with="db-skip-locked" default="handlers">
-        <handler id="handler_0" tags="handlers"/>
-        <handler id="handler_1" tags="handlers"/>
-        <handler id="handler_2" tags="handlers"/>
-        <handler id="handler_3" tags="handlers"/>
-    </handlers>
-
-    <destinations default="local">
-        <destination id="local" runner="local"/>
-        <destination id="gce_multicore" runner="local">
-            <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
-        </destination>
-        <destination id="bowtie" runner="local">
-             <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
-        </destination>
-        <destination id="single" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-            <param id="type">python</param>
-            <param id="nativeSpecification">--partition=debug --ntasks=1</param>
-            <param id="docker_sudo">false</param>
-            <param id="docker_volumes_from">galaxy</param>
-        </destination>
-        <destination id="double" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-            <param id="type">python</param>
-            <param id="nativeSpecification">--partition=debug --ntasks=2</param>
-            <param id="docker_sudo">false</param>
-            <param id="docker_volumes_from">galaxy</param>
-        </destination>
-        <destination id="cluster_4" runner="slurm">
-            <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-            <param id="type">python</param>
-            <param id="nativeSpecification">--partition=debug --ntasks=4</param>
-            <param id="docker_sudo">false</param>
-            <param id="docker_volumes_from">galaxy</param>
-        </destination>
-        <destination id="cluster_8" runner="slurm">
-           <env file="/home/galaxy/galaxy/.venv/bin/activate" />
-           <param id="type">python</param>
-           <param id="nativeSpecification">--partition=debug --ntasks=8</param>
-           <param id="docker_sudo">false</param>
-           <param id="docker_volumes_from">galaxy</param>
-        </destination>
-    </destinations>
-<!-- we could avoid this section in a small local instance ! -->
-    <limits>
-        <limit type="destination_total_concurrent_jobs" id="single">8</limit>
-        <limit type="destination_total_concurrent_jobs" id="double">4</limit>
-        <limit type="destination_total_concurrent_jobs" id="cluster_4">2</limit>
-        <limit type="destination_total_concurrent_jobs" id="cluster_8">1</limit>
-
-
-        <limit type="anonymous_user_concurrent_jobs">1</limit>
-
-        <limit type="destination_user_concurrent_jobs" id="single">8</limit>
-        <limit type="destination_user_concurrent_jobs" id="double">4</limit>
-        <limit type="destination_user_concurrent_jobs" id="cluster_4">2</limit>
-        <limit type="destination_user_concurrent_jobs" id="cluster_8">1</limit>
-
-    </limits>
-   <tools>
-        <tool id="sam_to_bam" destination="double"/>
-        <tool id="bowtie" destination="cluster_4"/>
-        <tool id="bowtieForSmallRNA" destination="cluster_4"/>
-        <tool id="bowtie_wrapper" destination="cluster_4"/>
-        <tool id="mircounts" destination="double"/>
-        <tool id="picard_SamToFastq" destination="cluster_2" />
-        <tool id="rna_star" destination="cluster_4"/>
-        <tool id="rna_starsolo" destination="cluster_4"/>
-        <tool id="samtools_cram_to_bam" destination="double"/>
-        <tool id="samtools_slice_bam" destination="double"/>
-        <tool id="samtools_view" destination="cluster_4"/>
-        <tool id="samtools_rmdup" destination="cluster_4"/>
-        <tool id="samtools_fastx" destination="cluster_4"/>
-        <tool id="samtool_filter2" destination="double"/>
-        <tool id="small_rna_maps" destination="double"/>
-        <tool id="sr_bowtie_dataset_annotation" destination="cluster_4"/>
-        <tool id="tp_grep_tool" destination="single" />
-   </tools>
-</job_conf>
diff --git a/environments/dev_mississippi/files/galaxy/config/job_conf.yml b/environments/dev_mississippi/files/galaxy/config/job_conf.yml
new file mode 100644
index 0000000..0b47e98
--- /dev/null
+++ b/environments/dev_mississippi/files/galaxy/config/job_conf.yml
@@ -0,0 +1,112 @@
+# This file is managed by Ansible.
+# Do not edit this file manually. Any changes will be automatically reverted.
+
+runners:
+  slurm:
+    load: galaxy.jobs.runners.slurm:SlurmJobRunner
+    drmaa_library_path: /usr/lib/slurm-drmaa/lib/libdrmaa.so
+
+handling:
+  assign:
+    - db-skip-locked
+  processes:
+    handler0:
+    handler1:
+    handler2:
+    handler3:
+
+execution:
+  default: cluster_1
+  environments:
+    cluster_1:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=1"
+    cluster_2:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=2"
+    cluster_4:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=4"
+    cluster_8:
+      runner: slurm
+      nativeSpecification: "--partition=debug --ntasks=8"
+
+limits:
+  - type: anonymous_user_concurrent_jobs
+    value: '1'
+  - type: registered_user_concurrent_jobs
+    value: '8'
+
+  - type: environment_total_concurrent_jobs
+    id: cluster_1
+    value: 12
+  - type: environment_total_concurrent_jobs
+    id: cluster_2
+    value: 6
+  - type: environment_total_concurrent_jobs
+    id: cluster_4
+    value: 3
+  - type: environment_total_concurrent_jobs
+    id: cluster_8
+    value: 2
+
+tools:
+  - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
+    environment: cluster_1
+
+  - id: "bowtie_index_builder_data_manager"
+    destination: "cluster_1"
+
+  - id: "retrieve_fasta_from_NCBI"
+    destination: "cluster_1"
+
+  - id: "sam_to_bam"
+    destination: "cluster_4"
+
+  - id: "bowtieForSmallRNA"
+    destination: "cluster_4"
+
+  - id: "bowtie_wrapper"
+    destination: "cluster_8"
+
+  - id: "fastqc"
+    destination: "cluster_2"
+
+  - id: "mircounts"
+    destination: "cluster_2"
+
+  - id: "picard_SamToFastq"
+    destination: "cluster_1" 
+
+  - id: "rna_star"
+    destination: "cluster_8"
+
+  - id: "rna_starsolo"
+    destination: "cluster_8"
+
+  - id: "samtools_cram_to_bam"
+    destination: "cluster_4"
+
+  - id: "samtools_slice_bam"
+    destination: "cluster_2"
+
+  - id: "samtools_view"
+    destination: "cluster_4"
+
+  - id: "samtools_rmdup"
+    destination: "cluster_4"
+
+  - id: "samtools_fastx"
+    destination: "cluster_4"
+
+  - id: "samtool_filter2"
+    destination: "cluster_2"
+
+  - id: "small_rna_maps"
+    destination: "cluster_2"
+
+  - id: "sr_bowtie_dataset_annotation"
+    destination: "cluster_4"
+
+  - id: "tp_grep_tool"
+    destination: "cluster_1" 
diff --git a/environments/dev_mississippi/files/galaxy/html/images/biotechno_M2_logo.png b/environments/dev_mississippi/files/galaxy/html/images/biotechno_M2_logo.png
deleted file mode 100644
index ab1ab5e..0000000
Binary files a/environments/dev_mississippi/files/galaxy/html/images/biotechno_M2_logo.png and /dev/null differ
diff --git a/environments/dev_mississippi/files/galaxy/html/images/galaxyXpand_logo.png b/environments/dev_mississippi/files/galaxy/html/images/galaxyXpand_logo.png
new file mode 100644
index 0000000..4dd0a71
Binary files /dev/null and b/environments/dev_mississippi/files/galaxy/html/images/galaxyXpand_logo.png differ
diff --git a/environments/dev_mississippi/files/galaxy/html/images/mississippi_dev.png b/environments/dev_mississippi/files/galaxy/html/images/mississippi_dev.png
new file mode 100644
index 0000000..247b531
Binary files /dev/null and b/environments/dev_mississippi/files/galaxy/html/images/mississippi_dev.png differ
diff --git a/environments/dev_mississippi/files/galaxy/html/welcome.html b/environments/dev_mississippi/files/galaxy/html/welcome.html
index fc231a6..57220f7 100644
--- a/environments/dev_mississippi/files/galaxy/html/welcome.html
+++ b/environments/dev_mississippi/files/galaxy/html/welcome.html
@@ -25,26 +25,16 @@
 <body>
     <div class="document">
             <p align="center">
-                <img src="images/biotechno_M2_logo.png" width="800" />
+                <img src="images/mississippi_dev.png" width="800" />
             </p>
         <hr/>
         <!-- -->
         <div class="alert alert-success" style="margin-top: 0.5em">
-            <h4>This Galaxy server instance is deployed with Ansible
+            <h4>This is a development Galaxy server to test
             <a href="/artbio/galaxyXpand"> galaxyXpand</a>. </h4>
             <div>
-                <p>For better resilience to troubles, the deployment of the Galaxy server dedicated to our users is
-                    now automated using the <a href="/ARTbio/GalaxyKickStart" target="_blank"> GalaxyKickStart Ansible Playbook</a>.
-                </p>
-                <p>Therefore, trainers and trainnees with an account on this (public) server may request any tool installation by raising
-                   a pull request after editing the
-                   <a href="/ARTbio/GalaxyKickStart/blob/master/extra-files/Analyse_genomes/analyse_genomes_tool_list.yml" target="_blank">
-                    analyse_genomes_tool_list.yml</a> on our <a href="/ARTbio/GalaxyKickStart" target="_blank"> GitHub GalaxyKickStart </a> repository.
-                </p>
-                <p>They may also simply raise an  issue on the <a href="/ARTbio/Run-Galaxy/issues/new/choose" target="_blank">
-                   Run-Galaxy GitHub repository</a>, poking @drosofff in the issue message: I'll be warned and try to rescue as fast as possible...
-                </p>
-            </div>
+                <p>User accounts may be deleted or reset at any time.</p>
+                <p>We therefore strongly discourage you to use it, unless you have been invited to do it.</p>
         </div>
         <!--
         <div class="row">
diff --git a/environments/dev_mississippi/group_vars/all/galaxy b/environments/dev_mississippi/group_vars/all/galaxy
index a089c56..a2570a7 100644
--- a/environments/dev_mississippi/group_vars/all/galaxy
+++ b/environments/dev_mississippi/group_vars/all/galaxy
@@ -5,20 +5,21 @@ galaxy_create_user: true
 galaxy_separate_privileges: true
 galaxy_privsep_user: "{{ galaxy_user }}"
 galaxy_layout: legacy
+galaxy_root: /home/galaxy
 galaxy_server_dir: "{{ galaxy_root }}/galaxy"
+galaxy_user: {name: galaxy, shell: /bin/bash}
 galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
 galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
 galaxy_config_dir: "{{ galaxy_server_dir }}/config"
 galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
-galaxy_root: /home/galaxy
-galaxy_user: {name: galaxy, shell: /bin/bash}
-galaxy_commit_id: release_22.05
+galaxy_commit_id: release_23.0
 galaxy_force_checkout: true
+miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
+miniconda_version: 23.9
+miniconda_channels: ['conda-forge', 'defaults']
 galaxy_tool_dependency_dir: "{{ galaxy_server_dir }}/../tool_dependencies"
 galaxy_manage_cleanup: yes  # Install a cron job to clean up Galaxy framework and job execution temporary
-miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
-miniconda_version: 4.7.12
-miniconda_manage_dependencies: false
+
 galaxy_config:
   galaxy:
     brand: "🧬 Mississippi-Dev"
@@ -72,20 +73,35 @@ galaxy_config:
           33373537623161643831626130393363353664343035613533333536623666396636393932356433
           6434343033353438613437353164623161383961323562313739
     tool_data_path: "{{ galaxy_server_dir }}/tool-data"
-    job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
-    allow_user_impersonation: true
-    allow_user_dataset_purge: true
-    enable_quotas: true
-    allow_user_deletion: true
+    job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
     allow_library_path_paste: true
     watch_tool_data_dir: true
+    # File serving perfomance
     nginx_x_accel_redirect_base: /_x_accel_redirect
+    # SQL Performance
+    slow_query_log_threshold: 5
+    enable_per_request_sql_debugging: true
+    # Automation / Ease of Use / User-facing features
+    allow_user_dataset_purge: true
+    enable_quotas: true
+    allow_user_deletion: true
+    allow_user_impersonation: true
+    watch_job_rules: 'auto'
+    allow_path_paste: true
+    expose_user_name: true
     expose_dataset_path: true
     expose_potentially_sensitive_job_metrics: true
     require_login: true
+    # Debugging
+    cleanup_job: onsuccess
+    # Tool security
+    outputs_to_working_directory: true
+    new_user_dataset_access_role_default_private: true # Make datasets private by default
   gravity:
+    process_manager: systemd
     galaxy_root: "{{ galaxy_server_dir }}"
-    app_server: gunicorn
+    galaxy_user: "{{ galaxy_user_name }}"
+    virtualenv: "{{ galaxy_venv_dir }}"
     gunicorn:
       # listening options
       bind: "unix:{{ galaxy_config_dir }}/gunicorn.sock"
@@ -106,12 +122,14 @@ galaxy_config:
 
 # deploy galaxy configuration files
 galaxy_config_files:
-  - src: environments/dev_mississippi/files/galaxy/config/job_conf.xml
+  - src: environments/dev_mississippi/files/galaxy/config/job_conf.yml
     dest: "{{ galaxy_config.galaxy.job_config_file }}"
   - src: environments/dev_mississippi/files/galaxy/html/welcome.html
     dest: "{{ galaxy_server_dir }}/static/welcome.html"
-  - src: environments/dev_mississippi/files/galaxy/html/images/biotechno_M2_logo.png
-    dest: "{{ galaxy_server_dir }}/static/biotechno_M2_logo.png"
+
+# deploy png galaxyXpand logo
+  - src: environments/dev_mississippi/files/galaxy/html/images/mississippi_dev.png
+    dest: "{{ galaxy_server_dir }}/static/images/mississippi_dev.png"
 
 # systemd
 galaxy_manage_systemd: true
diff --git a/environments/dev_mississippi/group_vars/all/nginx b/environments/dev_mississippi/group_vars/all/nginx
index 38a2b49..5ecaa40 100644
--- a/environments/dev_mississippi/group_vars/all/nginx
+++ b/environments/dev_mississippi/group_vars/all/nginx
@@ -1,6 +1,7 @@
 ---
 # NGINX
 nginx_server_src_dir: environments/dev_mississippi/templates/nginx/
+nginx_selinux_allow_local_connections: true
 nginx_ssl_servers:
   - galaxy
 nginx_enable_default_server: false
diff --git a/environments/dev_mississippi/group_vars/all/slurm b/environments/dev_mississippi/group_vars/all/slurm
index fa99095..e5c73be 100644
--- a/environments/dev_mississippi/group_vars/all/slurm
+++ b/environments/dev_mississippi/group_vars/all/slurm
@@ -11,3 +11,14 @@ slurm_config:
   SelectType: select/cons_res
   SelectTypeParameters: CR_Core_Memory
 
+slurm_nodes:
+  - name: "localhost"
+    CPUs: 16
+    RealMemory: 96617
+
+slurm_partitions:
+  - name: debug
+    Default: YES
+    DefMemPerCPU: 6038
+    Nodes: "localhost"
+
diff --git a/environments/dev_mississippi/group_vars/dbservers.yml b/environments/dev_mississippi/group_vars/dbservers.yml
new file mode 120000
index 0000000..2ef78cc
--- /dev/null
+++ b/environments/dev_mississippi/group_vars/dbservers.yml
@@ -0,0 +1 @@
+../../dbservers.yml
\ No newline at end of file
diff --git a/environments/dev_mississippi/hosts b/environments/dev_mississippi/hosts
index 4896183..fd86c21 100644
--- a/environments/dev_mississippi/hosts
+++ b/environments/dev_mississippi/hosts
@@ -1,3 +1,6 @@
 [dev_mississippi]
-
 localhost  ansible_connection=local ansible_user=root
+
+[dbservers:children]
+dev_mississippi
+
diff --git a/environments/dev_mississippi/templates/nginx/galaxy.j2 b/environments/dev_mississippi/templates/nginx/galaxy.j2
index 60a3836..34ce2ef 100644
--- a/environments/dev_mississippi/templates/nginx/galaxy.j2
+++ b/environments/dev_mississippi/templates/nginx/galaxy.j2
@@ -16,6 +16,10 @@ server {
     # The virtualhost is our domain name
     server_name   "{{ inventory_hostname }}";
 
+    proxy_read_timeout 300;
+    proxy_connect_timeout 300;
+    proxy_send_timeout 300; 
+
     # Our log files will go here.
     access_log /var/log/nginx/access.log;
     error_log /var/log/nginx/error.log;
diff --git a/playbook.yml b/playbook.yml
index 90a6c1c..1ed9007 100644
--- a/playbook.yml
+++ b/playbook.yml
@@ -1,10 +1,22 @@
 ---
+- hosts: dbservers
+  become: true
+  become_user: root
+  pre_tasks:
+    - name: Install Dependencies
+      package:
+        name: 'acl'
+  roles:
+    - galaxyproject.postgresql
+    - role: galaxyproject.postgresql_objects
+      become: true
+      become_user: postgres
+
 - hosts: all
   become: true
   become_user: root
 
   pre_tasks:
-
     - name: Add custom slurm PPA (used for Slurm DRMAA package)
       apt_repository:
         repo: ppa:natefoo/slurm-drmaa
@@ -19,37 +31,29 @@
           - 'bzip2'
           - 'git'
           - 'make'
-          - 'python3-psycopg2'
           -  'tar'
-          - 'virtualenv'
+          - 'python3-venv'
+          - 'python3-setuptools'
           - slurm-wlm
           - slurm-drmaa-dev
           - python-psutil
 
   roles:
-    - role: clean_galaxykickstart
-      when: galaxykickstart_to_gravity
-    - role: galaxyproject.postgresql
-      when: install_postgresql
-    - role: galaxyproject.postgresql_objects
-      become: true
-      become_user: postgres
-    - geerlingguy.pip
     - galaxyproject.galaxy
-    - role: uchida.miniconda
+    - role: galaxyproject.miniconda
       become: true
       become_user: "{{ galaxy_user.name }}"
     - galaxyproject.nginx
-    - role: ansible-slurm
+    - role: galaxyproject.slurm
       become: true
       when: install_slurm
     - role: installUptime
       when: install_uptime
 
-  post_tasks:
-
-    - name: restart nginx
-      service:
-        name: nginx
-        state: restarted
-      when: not nginx_supervisor
+#  post_tasks:
+#
+#    - name: restart nginx
+#      service:
+#        name: nginx
+#        state: restarted
+#      when: not nginx_supervisor
diff --git a/requirements.yml b/requirements.yml
index 15c7b90..775c6fa 100644
--- a/requirements.yml
+++ b/requirements.yml
@@ -1,18 +1,14 @@
-- src: https://github.com/ARTbio/ansible-galaxy.git
-  name: galaxyproject.galaxy
-  version: galaxyXpand
+- src: galaxyproject.galaxy
+  version: 0.10.19
 - src: galaxyproject.nginx
-  version: 0.7.0
+  version: 0.7.1
 - src: galaxyproject.postgresql
-  version: 1.0.3
+  version: 1.1.2
 - src: galaxyproject.postgresql_objects
-  version: 1.1.0
-- src: geerlingguy.pip
-  version: 2.0.0
-- src: uchida.miniconda
-  version: 0.3.0
-- src: https://github.com/ARTbio/ansible-slurm.git
-  name: ansible-slurm
-  version: artbio
+  version: 1.2.0
+- src: galaxyproject.miniconda
+  version: 0.3.1
+- src: galaxyproject.slurm
+  version: 1.0.4
 - src: https://github.com/ARTbio/ansible-galaxy-tools.git
   name: install.galaxy-tools
diff --git a/roles/clean_galaxykickstart/defaults/main.yml b/roles/clean_galaxykickstart/defaults/main.yml
deleted file mode 100644
index 9cb27fd..0000000
--- a/roles/clean_galaxykickstart/defaults/main.yml
+++ /dev/null
@@ -1 +0,0 @@
-galaxykickstart_to_gravity: yes
\ No newline at end of file
diff --git a/roles/clean_galaxykickstart/tasks/clean.yml b/roles/clean_galaxykickstart/tasks/clean.yml
deleted file mode 100644
index d0eb254..0000000
--- a/roles/clean_galaxykickstart/tasks/clean.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-- name: Stop all supervisorctl processes
-  supervisorctl:
-    name: all
-    state: absent
-
-- name: Stop and deregister supervisorctl
-  ansible.builtin.systemd:
-    name: supervisor.service
-    state: stopped
-    enabled: false
-
-- name: Stop and deregister slurmctld
-  ansible.builtin.systemd:
-    name: slurmctld.service
-    state: stopped
-    enabled: false
-
-- name: Stop and deregister slurmd
-  ansible.builtin.systemd:
-    name: slurmd.service
-    state: stopped
-    enabled: false
-
-- name: Remove and purge supervisor
-  ansible.builtin.apt:
-    name: supervisor
-    state: absent
-    purge: true
-
-- name: Remove and purge munge
-  ansible.builtin.apt:
-    name: munge
-    state: absent
-    purge: true
-
-- name: Remove and purge nginx
-  ansible.builtin.apt:
-    name: nginx-common
-    state: absent
-    purge: true
diff --git a/roles/clean_galaxykickstart/tasks/main.yml b/roles/clean_galaxykickstart/tasks/main.yml
deleted file mode 100644
index 46cd98e..0000000
--- a/roles/clean_galaxykickstart/tasks/main.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-- name: include cleaning tastk when asked
-  import_tasks:
-    file: clean.yml
-  when: galaxykickstart_to_gravity
diff --git a/roles/installUptime/defaults/main.yml b/roles/installUptime/defaults/main.yml
index 10bd812..47b6b2d 100644
--- a/roles/installUptime/defaults/main.yml
+++ b/roles/installUptime/defaults/main.yml
@@ -1,8 +1,10 @@
-install_uptime: yes
+install_uptime: no
+uptime_dir: "{{ galaxy_root }}"
+uptime_user: "{{ galaxy_user.name }}"
+service_description: "A service to run uptime.sh and publish server usage image through galaxy nginx"
+
 uptime_templates:
-  - src: uptime.conf.j2
-    dest: "{{ galaxy_gravity_state_dir }}/supervisor/supervisord.conf.d/_default_.d/uptime.conf"
   - src: uptime.R.j2
-    dest: "{{ galaxy_gravity_state_dir }}/uptime.R"
+    dest: "{{ uptime_dir }}/uptime.R"
   - src: uptime.sh.j2
-    dest: "{{ galaxy_gravity_state_dir }}/uptime.sh"
+    dest: "{{ uptime_dir }}/uptime.sh"
diff --git a/roles/installUptime/tasks/install_uptime.yml b/roles/installUptime/tasks/install_uptime.yml
index 9946db3..8d792c5 100644
--- a/roles/installUptime/tasks/install_uptime.yml
+++ b/roles/installUptime/tasks/install_uptime.yml
@@ -3,16 +3,27 @@
     name:
       - 'r-base'
 
+- name: Create an uptime directory
+  become_user: "{{ uptime_user }}"
+  file:
+    path: "{{ galaxy_root }}"
+    state: directory
+
 - name: Instantiate uptime templates
-  become_user: 'galaxy'
+  become_user: "{{ uptime_user }}"
   template:
     src: "{{ item.src }}"
     dest: "{{ item.dest }}"
     force: yes
     mode: "{{ galaxy_config_perms }}"
   with_items: "{{ uptime_templates }}"
+  
+- name: Create uptime systemd service file
+  template:
+    src: templates/uptime.service.j2
+    dest: /lib/systemd/system/uptime.service
 
-- name: galaxyctl supervisorctl reload
-  command: "{{ galaxy_venv_dir }}/bin/galaxyctl supervisorctl reload"
-  environment:
-    GRAVITY_STATE_DIR: "{{ galaxy_gravity_state_dir }}"
+- name: Start uptime service
+  systemd:
+    name: uptime
+    state: started
diff --git a/roles/installUptime/tasks/main.yml b/roles/installUptime/tasks/main.yml
index 9fa3bd4..32677a8 100644
--- a/roles/installUptime/tasks/main.yml
+++ b/roles/installUptime/tasks/main.yml
@@ -1,4 +1,4 @@
-- name: include cleaning tastk when asked
+- name: include uptime appli when asked
   import_tasks:
     file: install_uptime.yml
   when: install_uptime
diff --git a/roles/installUptime/templates/uptime.conf.j2 b/roles/installUptime/templates/uptime.conf.j2
deleted file mode 100644
index 978c31e..0000000
--- a/roles/installUptime/templates/uptime.conf.j2
+++ /dev/null
@@ -1,11 +0,0 @@
-[program:uptime]
-command         = /bin/bash -c "sh {{ galaxy_gravity_state_dir }}/uptime.sh"
-umask           = 022
-autostart       = true
-autorestart     = true
-user            = galaxy
-stopasgroup     = true
-killasgroup     = true
-stopsignal      = KILL
-stdout_logfile  = {{ galaxy_gravity_state_dir }}/log/uptime_service.log
-redirect_stderr = true
diff --git a/roles/installUptime/templates/uptime.service.j2 b/roles/installUptime/templates/uptime.service.j2
new file mode 100644
index 0000000..0cce560
--- /dev/null
+++ b/roles/installUptime/templates/uptime.service.j2
@@ -0,0 +1,11 @@
+[Unit]
+Description={{ service_description }}
+
+[Service]
+Type=simple
+User={{ uptime_user }}
+ExecStart=/bin/bash -c "sh {{ uptime_dir }}/uptime.sh"
+Restart=on-failure
+
+[Install]
+WantedBy=multi-user.target
\ No newline at end of file
diff --git a/roles/installUptime/templates/uptime.sh.j2 b/roles/installUptime/templates/uptime.sh.j2
index eb33f4f..eab2e3d 100644
--- a/roles/installUptime/templates/uptime.sh.j2
+++ b/roles/installUptime/templates/uptime.sh.j2
@@ -2,8 +2,8 @@
 # uptime.sh
 while true
 do
-  echo `date +"%Y/%m/%d %H:%M:%S"; cat /proc/loadavg` >> {{ galaxy_gravity_state_dir }}/log/uptime.log
-  tail -n 4032 {{ galaxy_gravity_state_dir }}/log/uptime.log > {{ galaxy_gravity_state_dir }}/log/lastuptime.log
-  Rscript {{ galaxy_gravity_state_dir }}/uptime.R {{ galaxy_gravity_state_dir }}/log/lastuptime.log 2>&1 >/dev/null
+  echo `date +"%Y/%m/%d %H:%M:%S"; cat /proc/loadavg` >> {{ uptime_dir }}/uptime.log
+  tail -n 4032 {{ uptime_dir }}/uptime.log > {{ uptime_dir }}/lastuptime.log
+  Rscript {{ uptime_dir }}/uptime.R {{ uptime_dir }}/lastuptime.log 2>&1 >/dev/null
   sleep 300
 done