Use local tool dirs

[lldelisle]

Hi,
I noticed that when you use directories for your local tool instead of just a xml (for example, if you need another python script), it will not update the local_tool_conf.xml:

ansible-galaxy/templates/local_tool_conf.xml.j2

Lines 4 to 6 in a834b46

	{% if tool.endswith('.xml') %}
	<tool file="{{ tool }}" />
	{% endif %}

In my case I put in my group_var:

galaxy_local_tools:
  - splitbedGraphFromBed
  - ScaleBedGraph

And I have:

$ tree files/galaxy/tools/
files/galaxy/tools/
├── ScaleBedGraph
│   ├── ScaleBedGraph.sh
│   └── ScaleBedGraph.xml
└── splitbedGraphFromBed
    ├── splitbedGraphFromBed.py
    └── splitbedGraphFromBed.xml

2 directories, 4 files

Then I needed to put a templates/galaxy/config/tool_conf.xml.j2 with all the default tools + at the end:

  <section id="LDtools" name="LDtools">
    <tool file="{{ galaxy_local_tools_dir }}/splitbedGraphFromBed/splitbedGraphFromBed/splitbedGraphFromBed.xml" />
    <tool file="{{ galaxy_local_tools_dir }}/ScaleBedGraph/ScaleBedGraph/ScaleBedGraph.xml" />
  </section>

Were there a better way?
Something like:

{% for tool in galaxy_local_tools %}
{% if not tool.endswith('.xml') %}
    <tool file="{{ galaxy_local_tools_dir }}/{{ tool }}/{{ tool }}/{{ tool }}.xml" />
{% endif %}
{% endfor %}

?
Also I found a bit strange there the tool directory is put in a directory tool...

[elichad]

I just ran into this also. It would be useful for the local tool template to loop through the tool directory looking for XML files if you can determine that it's a directory and not an XML file, but I don't know if that's within the scope of possibility with the templates.

I'll also use a custom tool_conf.xml.j2 template to work around this for now.

[jarrah42]

Changing tasks/static_setup.yml as follows may fix the directory in directory problem:

    - name: Install local tools
      copy:
        src: "{{ galaxy_local_tools_src_dir }}/{{ item }}"
        dest: "{{ galaxy_local_tools_dir }}"
        mode: preserve
      with_items: "{{ galaxy_local_tools | default([]) }}"
      when: galaxy_local_tools is defined