Add deeparg

[hugolefeuvre]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[hugolefeuvre]

Problem when using deepARG in a container with the Theano package: IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO'
This problem has already been reported and closed in this issue: nf-core/funcscan#23 but there's no clear explanation of how they solved the problem, so I have restarted the discussion to try to get more information.

[jfy133]

Just so it doesn't get lost in the closed funcscan thread:

We ended up mounting a dummy file (the bash binary of the execution node) but with the name PKG_INFO:

https://github.com/nf-core/funcscan/blob/master/modules%2Fnf-core%2Fdeeparg%2Fpredict%2Fmain.nf#L10-L18

Also I see lower down in the script execution that we also make a directory for theanos which you may also have to do for cases of singularity (if you use that)

    # Theano needs a writable space and uses the home directory by default,
    # but the latter is not always writable, for instance when Singularity
    # is run in --no-home mode
    mkdir -p theano
    export THEANO_FLAGS="base_compiledir=\$PWD/theano"

deeparg predict <...>

I hope that helps/works for you!

[hugolefeuvre]

Thank you for your answer @jfy133 ! I'll see if it works for me !

[bgruening]

I did something here, but forgot what I wanted to do ;)

maybe useful hugolefeuvre#1 ?

[hugolefeuvre]

I did something here, but forgot what I wanted to do ;)

maybe useful hugolefeuvre#1 ?

It was maybe about the message I send on galaxy-iuc on Element ?

Hello, is it possible to add a parameter for the docker run launched in the git tests ? Like --docker_run_extra_arguments which I can use for a planemo test --biocontainers
This would be useful for the deepARG wrapper, as the tool fails in a container and requires this parameter to be added in order to work: -v $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO
Thank you !

And you answered

I think this is possible, but we should fix the container that is a hack at its best.

But beyond that I think it can be useful in any case.

[bgruening]

Thanks a lot @hugolefeuvre its now green.
I added a few more comments, they apply to both tools :)

[bgruening]

@bernt-matthias can you maybe look at the DM bits here?

[bernt-matthias]

Can we use @TOOL_VERSION@ here instead of 1.0.4?

Do you know if the tool can also download other versions. Do you know if future versions can use older downloads?

[hugolefeuvre]

Yes I think we can.
The tool download all the versions (v1 and v2), and then you can choose version with a deeparg predict parameter --model-version
There is no information if future versions can use older downloads, actually all the versions are in the zenodo that is download by deeparg as database.

[bernt-matthias]

Can you share a link to the zenodo record?

[hugolefeuvre]

https://zenodo.org/records/8280582

[bernt-matthias]

Should we filter for the version here?

[hugolefeuvre]

What type of filter did you have in mind?

[bernt-matthias]

I was thinking to filter for the version, such that the corresponding tool version can only process the values generated with exactly this version .. not sure if it makes sense.

[hugolefeuvre]

To make sure that the only DB that can be used is the one that corresponds to the version of the tool?
Someting like that ? <filter column="version" value="@TOOL_VERSION@"/>