Merge pull request #877 from usegalaxy-eu/311

Use Python 3.11 by default and venv instead of virtualenv
usegalaxy-eu · Aug 31, 2023 · 80de267 · 80de267
2 parents 75424ab + d7cf983
commit 80de267
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Showing 4 changed files with 19 additions and 6 deletions.
diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml
@@ -25,6 +25,9 @@ autofs_mount_points:
   - jwd
   - usrlocal
 
+# Miniconda role variables (galaxyproject.miniconda)
+conda_prefix: /opt/miniconda
+
 # fs-maintenance
 fsm_maintenance_dir: "/data/dnb01/maintenance"
 fsm_cron_tasks:
@@ -247,7 +250,7 @@ condor_extra: |
 gie_proxy_dir: "{{ galaxy_root }}/gie-proxy/proxy"
 gie_proxy_git_version: main
 gie_proxy_setup_nodejs: nodeenv
-gie_proxy_virtualenv_command: /usr/bin/python3 -m virtualenv #"{{ pip_virtualenv_command }}"
+gie_proxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies" #"{{ pip_virtualenv_command }}"
 gie_proxy_nodejs_version: "10.13.0"
 gie_proxy_virtualenv: "{{ galaxy_root }}/gie-proxy/venv"
 gie_proxy_setup_service: systemd
@@ -312,7 +315,7 @@ galaxy_venv_dir: "{{ galaxy_root }}/venv"
 galaxy_job_working_directory: "{{ galaxy_config['galaxy']['job_working_directory'] }}"
 ucsc_build_sites:
 
-galaxy_virtualenv_command: "pyvenv"
+galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies"
 #galaxy_virtualenv_python: "python3.6"
 galaxy_nonrepro_tools: "{{ galaxy_root }}/custom-tools"
 galaxy_nonrepro_commit: master

diff --git a/group_vars/sn07.yml b/group_vars/sn07.yml
@@ -279,7 +279,7 @@ condor_extra: |
 gie_proxy_dir: "{{ galaxy_root }}/gie-proxy/proxy"
 gie_proxy_git_version: main
 gie_proxy_setup_nodejs: nodeenv
-gie_proxy_virtualenv_command: /usr/bin/python3 -m virtualenv #"{{ pip_virtualenv_command }}"
+gie_proxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies" #"{{ pip_virtualenv_command }}"
 gie_proxy_nodejs_version: "10.13.0"
 gie_proxy_virtualenv: "{{ galaxy_root }}/gie-proxy/venv"
 gie_proxy_setup_service: systemd
@@ -350,7 +350,7 @@ 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/virtualenv"
+galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies"
 galaxy_nonrepro_tools: "{{ galaxy_root }}/custom-tools"
 galaxy_nonrepro_commit: master
 

diff --git a/sn06.yml b/sn06.yml
@@ -134,6 +134,17 @@
         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/sn06.yml
+    - role: galaxyproject.miniconda
+      vars:
+        miniconda_prefix: "{{ conda_prefix }}"
+        galaxy_conda_create_env: true
+        galaxy_conda_env_packages:
+          - python=3.11
+          - pip
+
     - usegalaxy-eu.autoupdates # keep all of our packages up to date
     - influxdata.chrony # Keep our time in sync.
 

diff --git a/sn07.yml b/sn07.yml
@@ -188,9 +188,8 @@
         miniconda_prefix: "{{ conda_prefix }}"
         galaxy_conda_create_env: true
         galaxy_conda_env_packages:
-          - python=3.8
+          - python=3.11
           - pip
-          - virtualenv
 
     - usegalaxy-eu.autoupdates # keep all of our packages up to date
     - influxdata.chrony # Keep our time in sync.