Support PATH_TO_IMAGES in vanilla Galaxy tools.

[jmchilton]

Currently only works for tool shed installed tools, differing behavior for tool shed installed tools and vanilla tools drives me crazy 😄.

https://twitter.com/dpryan79/status/695254422956425216

[nsoranzo]

👍

[pvanheus]

Similar request from here: https://biostar.usegalaxy.org/p/18371/ - as I proposed, possible an API call could provide a link to images/ in the tool dir?

[pjbriggs]

I don't think this issue has anything to do with the use of $PATH_TO_IMAGES (which is not actually required anyway, see e.g. galaxy-iuc/standards#46) - it's more generally about how Galaxy handles the .. image:: directive in the tool help.

As far as I can make out, Galaxy only seems to process the directive for tools which have been installed via a toolshed - specifically in the __inititalize_help method of the Tool class in lib/galaxy/tools/__init__.py:

    ...
    help_text = tool_source.parse_help()
    if help_text is not None:
        if self.repository_id and help_text.find( '.. image:: ' ) >= 0:
    ...

If I've understood this correctly then there would need to be some new code to handle when the tool is not an installed repository, coupled with some mechanism for actually serving the image file from wherever it is on the filesystem (as pointed out by @pvanheus). Could one possibility be to inline the images (e.g. base64 encode them)?

Either way I'd suggest change the title of this issue to remove the reference to $PATH_TO_IMAGES.

[SamGG]

Hi,
I am facing the same problem. What is the solution/workaround?
Best.

[SamGG]

My current workaround is to create a directory in /static/images/tools and copy the images there.
In the help section I can write:
.. image:: ${static_path}/images/tools/my_super_tool/my_workflow_image.png
And the image is rendered.

[pjbriggs]

Hello @SamGG it's been a while since I had this problem but I think I used the same workaround as you, if this helps.

[SamGG]

Thanks for sharing. Hope this will be fixed.