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remove miniconda from sn09 playbook and use the conda from /usr/local/tools/_conda for creating Python envs #1591

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Merged
merged 1 commit into from
Jul 27, 2025
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remove miniconda from sn09 playbook and use the conda from /usr/local/tools/_conda for creating Python envs #1591

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7 changes: 2 additions & 5 deletions group_vars/sn09/sn09.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,6 @@ autofs_mount_points:
- cache
- misc

# Miniconda role variables (galaxyproject.miniconda)
conda_prefix: /opt/miniconda

# Role: usegalaxy_eu.firewall
# NOTE: firewall_restart_daemon is set to false by default and it is deliberately set to false
# to avoid restarting the firewall daemon because the changes can possibly disrupt your only
Expand Down Expand Up @@ -259,7 +256,7 @@ galaxy_systemd_memory_limit_workflow: 15
gie_proxy_dir: '{{ galaxy_root }}/gie-proxy/proxy'
gie_proxy_git_version: v0.1.0
gie_proxy_setup_nodejs: nodeenv
gie_proxy_virtualenv_command: '{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies' #"{{ pip_virtualenv_command }}"
gie_proxy_virtualenv_command: '{{ galaxy_virtualenv_command }}'
gie_proxy_nodejs_version: '22.0.0'
gie_proxy_virtualenv: '{{ galaxy_root }}/gie-proxy/venv'
gie_proxy_setup_service: systemd
Expand Down Expand Up @@ -327,7 +324,7 @@ galaxy_venv_dir: '{{ galaxy_root }}/venv'
galaxy_job_working_directory: "{{ galaxy_config['galaxy']['job_working_directory'] }}"
ucsc_build_sites:

galaxy_virtualenv_command: '{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies'
galaxy_virtualenv_command: '/usr/local/tools/_conda/envs/__python@3.11.5/bin/python -m venv --copies'
galaxy_nonrepro_tools: '{{ galaxy_root }}/custom-tools'
galaxy_nonrepro_commit: master

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15 changes: 0 additions & 15 deletions sn09.yml
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Expand Up @@ -285,21 +285,6 @@
enable_pam_limits: true # Prevent out of control processes
enable_install_software: true # Some extra admin tools (*top, vim, etc)
- geerlingguy.repo-epel # Install EPEL repository

## Install miniconda, create a _galaxy_ environment and install Packages
## Galaxy will use the virtualenv from this conda environment (see
## galaxy_virtualenv_command) in the group_vars/sn09.yml
- role: galaxyproject.miniconda
vars:
miniconda_prefix: '{{ conda_prefix }}'
miniconda_distribution: 'miniconda'
miniconda_executable: 'conda'
galaxy_conda_create_env: true
galaxy_conda_env_packages:
- python=3.11.5
- pip
- libsqlite=3.43.0 #pinning this due to https://github.com/galaxyproject/ansible-galaxy/issues/228

- usegalaxy-eu.autoupdates # keep all of our packages up to date
- influxdata.chrony # Keep our time in sync.

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