migrate in emboss_5, fastqc, freebayes, picard from devteam

[martenson]

part of galaxyproject/tools-devteam#406
xref: #1060

ping @galaxyproject/iuc

this is an effort to address part of galaxyproject/tools-devteam#416

[martenson]

thanks to @erasche for helping with figuring out how to treat the missing docs

[martenson]

freebayes fails linting because of <conversion> not being allowed in schema https://docs.galaxyproject.org/en/latest/dev/schema.html

<param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm">
    <conversion name="Tabixized_input" type="tabix" />
</param>

ping @jmchilton - did we miss this tag?

[nsoranzo]

@martenson This a symlink to a file that is present only on the tools-devteam repository. Can you add it to the PR?

[nsoranzo]

I've added the file in commit 10954c0 .

[nsoranzo]

@martenson I've pushed 2 commits to your branch and I plan to do some more work tomorrow, hope that's OK.

[yhoogstrate]

Same for me (Just one pr)

[nsoranzo]

I made a massive clean-up of the EMBOSS wrappers in commit cafb44d . More can be done post-merge, e.g.:

• fix datatype assignment to output datasets
• change many type="select" params to boolean.

[nsoranzo]

freebayes fails linting because of <conversion> not being allowed in schema

@martenson @jmchilton I've created galaxyproject/galaxy#3453 to track this.

[nsoranzo]

@martenson I've added the changes requested in my review of martenson#1 .
@jmchilton If you can update Planemo with the new XSD changes, then the tests should pass.

[yhoogstrate]

@nsoranzo Can this be removed?

Edit: nope, emboss is not in bioconda

[nsoranzo]

It is not in Bioconda, but it is in iuc:

$ conda search emboss
Fetching package metadata ...............
emboss                       5.0.0                         0  iuc             
                             6.5.7                         0  bioconda        
                             6.5.7                         1  bioconda        
                             6.5.7                         2  bioconda        

Anyway, I have no strong opinion, maybe we can remove it when we upgrade to a newer EMBOSS version.

[martenson]

All tool tests are failing now, I don't know why.

[nsoranzo]

The problem was that release_16.10 has not been update to require six 1.10, but now that we have a twill wheel and a new Planemo release (thanks to @jmchilton), the linting passes and only the Java tools fail for same reason. @bgruening ideas?

[bgruening]

Nicola this looks wired, isn't it?

[nsoranzo]

Why? rgFastQC.py is part of the wrapper.

[bgruening]

Isn't it a string substitution: https://github.com/galaxyproject/galaxy/blob/29cdd6007fa333e8e9caa85a1fc58ae389405cf2/lib/galaxy/jobs/__init__.py#L983
and should be $__tool_directory__

[nsoranzo]

The curly braces should be fine, see https://docs.python.org/2/library/string.html#template-strings

[nsoranzo]

I think I've fixed the FastQC issue with commit d38e1e7, let's see.

[bgruening]

Oh ok! Good to know. I thought thats the reason for the strange error message. I still think we should change the variable name and keep is consistent with other places.
Thanks NIcola!

[martenson]

fastqc now passes, yay! thanks @nsoranzo

[nsoranzo]

So FastQC is finally fixed, but all Picard tools still fail because of this error: Exception in thread "main" java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine : Unsupported major.minor version 52.0

This indicates that Picard tools are run with Java <8 even if the correct java-jdk Bioconda package is installed. Maybe we need to use Galaxy 17.01? @bgruening

[nsoranzo]

The JAVA_HOME change was not applied during the Travis build, trying to close/reopen.

[bgruening]

Thanks @nsoranzo. Thats seems to fix it.
Ready for the merge?

[nsoranzo]

Green at last! Thanks all!

[martenson]

Splendid. Thanks @nsoranzo @bgruening and @yhoogstrate for help!