Auto update of requirements in virtualenv

[microfuge]

Dear All,

First of all thanks so much for this role!

I have used a modified version of this role to install Galaxy in a privilege separation mode. As the virtualenv is owned by a privsep user, galaxy (galaxy user) can not auto update the newly arising requirements in the virtualenv (e.g due to enabling new options in the config) .
For example the drmaa package is not installed by default. The option in the role defaults where the packages to install in the virtualenv seem to be mentioned here -

galaxy_requirements_file: "{{ galaxy_server_dir }}/lib/galaxy/dependencies/pinned-requirements.txt"

Should I add required packages (e.g drmaa ) to the pinned-requirements.txt in the Galaxy source ? Or is there a way that I have missed? Also is there a way to know which packages are not present when a new option is enabled in the configs. E.g when enabling cluster access in job config, the information that the drmaa package is missing and needs to be added.

Thanks Again and please let me know if something is missing/wrong in this post.
Regards,
Saurabh

[natefoo]

drmaa is a conditional dependency and is installed if a drmaa-backed runner plugin is enabled in Galaxy's job config. This happens in the role via these tasks in dependencies.yml:

    - name: Collect Galaxy conditional dependency requirement strings
      command: "{{ galaxy_venv_dir }}/bin/python -c \"import galaxy.dependencies; print('\\n'.join(galaxy.dependencies.optional('{{ galaxy_config_file }}')))\""
      environment:
        PYTHONPATH: "{{ galaxy_server_dir }}/lib"
      register: conditional_dependencies
      changed_when: no

    - name: Install Galaxy conditional dependencies
      pip:
        name: "{{ conditional_dependencies.stdout_lines }}"
        extra_args: "--index-url https://wheels.galaxyproject.org/simple/ --extra-index-url https://pypi.python.org/simple {{ pip_extra_args | default('') }}"
        virtualenv: "{{ galaxy_venv_dir }}"
        virtualenv_command: "{{ galaxy_virtualenv_command | default(pip_virtualenv_command | default(omit)) }}"
      environment:
        PYTHONPATH: null
        VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
      when: (not ansible_check_mode) and conditional_dependencies.stdout_lines | length > 0

If your job config file is written out prior to these tasks executing, it should have installed drmaa.

You can also add arbitrary packages to install in the list galaxy_additional_venv_packages.

[microfuge]

Hi Nate,

Thanks a ton!
The issue was caused by mismanagement of configs from my side and also me not checking the correct venv dir.

The role correctly and appropriately installs the requirements as they arise. Thanks also for pointing out the source snippets which are useful and answer all my queries.

Just to add, this role has been a lifesaver for me and thanks for creating/maintaining. I consider the issue closed from my side.