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genome_annotation_tools_3.yml
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genome_annotation_tools_3.yml
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---
# This is a sample file to be used as a reference for populating a list of
# tools that you wish to install into Galaxy from a Tool Shed via the
# `install_tool_shed_tools.py` script.
#
# For each tool you want to install, you must provide the following keys:
# * name: this is is the name of the tool to install
# * owner: owner of the Tool Shed repository from where the tools is being
# installed
# Further, you need to provide **one** of the following two keys:
# * tool_panel_section_id: ID of the tool panel section where you want the
# tool to be installed. The section ID can be found
# in Galaxy's `shed_tool_conf.xml` config file. Note
# that the specified section must exist in this file.
# Otherwise, the tool will be installed outside any
# section.
# * tool_panel_section_label: Display label of a tool panel section where
# you want the tool to be installed. If it does not
# exist, this section will be created on the target
# Galaxy instance (note that this is different than
# when using the ID).
# Multi-word labels need to be placed in quotes.
# Each label will have a corresponding ID created;
# the ID will be an all lowercase version of the
# label, with multiple words joined with
# underscores (e.g., 'BED tools' -> 'bed_tools').
#
# Tou can also specify the following optional keys to further define the
# installation properties:
# * tool_shed_url: the URL of the Tool Shed from where the tool should be
# installed. (default: https://toolshed.g2.bx.psu.edu)
# * revisions: a list of revisions of the tool, all of which will attempt to
# be installed. (default: latest)
# * install_tool_dependencies: True or False - whether to install tool
# dependencies or not. (default: True)
# * install_repository_dependencies: True or False - whether to install repo
# dependencies or not. (default: True)
api_key: fakekey
galaxy_instance: http://localhost:8080
install_resolver_dependencies: True
install_tool_dependencies: False
tools:
- name: blast_rbh
owner: peterjc
install_resolver_dependencies: False
install_repository_dependencies: False
tool_panel_section_label: "Similarity Search"
- name: blastxml_to_top_descr
owner: peterjc
install_repository_dependencies: False
tool_panel_section_label: "Similarity Search"
#- name: venn_list
#owner: peterjc
#tool_panel_section_label: "Visualisation"
- name: mummer
owner: peterjc
install_repository_dependencies: False
tool_panel_section_label: "Alignments"
- name: mira4_assembler
owner: peterjc
install_repository_dependencies: False
tool_panel_section_label: "Assembly"
- name: effectivet3
owner: peterjc
tool_panel_section_label: "Classification"
- name: nlstradamus
owner: peterjc
tool_panel_section_label: "Classification"
- name: diamond
owner: bgruening
install_resolver_dependencies: False
tool_panel_section_label: "Similarity Search"
- name: data_manager_diamond_database_builder
owner: bgruening
install_resolver_dependencies: False
tool_panel_section_label: "Similarity Search"
- name: suite_glimmer
owner: bgruening
tool_panel_section_label: "Gene Prediction"
- name: spades
owner: nml
tool_panel_section_label: "Assembly"
- name: rnaspades
owner: iuc
tool_panel_section_label: "Assembly"
- name: metaspades
owner: nml
tool_panel_section_label: "Assembly"
- name: cd_hit
owner: iuc
tool_panel_section_label: "Clustering"
- name: clustalw
owner: devteam
tool_panel_section_label: "Clustering"
- name: suite_tripal
owner: gga
tool_panel_section_label: "Tripal"
- name: suite_askomics
owner: gga
tool_panel_section_label: "Askomics"
- name: suite_apollo
owner: gga
tool_panel_section_label: "Apollo"
- name: weblogo3
owner: devteam
install_resolver_dependencies: False
tool_panel_section_label: "Visualisation"
- name: suite_chado
owner: gga
tool_panel_section_label: "Chado"