Updating tb-profiler to 6.4.0

[emarinier]

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)

Related to #5139

[emarinier]

Testing error appears to be:

[E::hts_open_format] Failed to open file "vcf/tbprofiler.targets.vcf.gz" : No such file or directory
Failed to read from vcf/tbprofiler.targets.vcf.gz: No such file or directory

and possibly:

[19:57:03] INFO     Running delly                                      bam.py:84
           ERROR    delly: error while loading shared libraries:    utils.py:534
                    libboost_iostreams.so.1.85.0: cannot open                   
                    shared object file: No such file or directory               
                                                                                
           ERROR    Delly failed, skipping                             bam.py:96

The delly-related error doesn't appear when run locally with planemo serve. However, it seems like a similar error has happened before for others with tb-profiler: jodyphelan/TBProfiler#88

[emarinier]

The solution appears to be fixing the version of delly:

<requirements>
    <requirement type="package" version="1.2.6">delly</requirement>
    <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
</requirements>

See these issues for some more information:

jodyphelan/TBProfiler#393 (comment)
jodyphelan/TBProfiler#371 (comment)

[bgruening]

@pvanheus do you want to have a look?

@emarinier thanks a lot

[bgruening]

If this is true, we should maybe fix the conda package.

[bgruening]

Oh delly is not even a dependency of tb-profiler. https://github.com/bioconda/bioconda-recipes/blob/master/recipes/tb-profiler/meta.yaml

It is a dependency of https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pathogen-profiler/meta.yaml

[bgruening]

I guess then we leave it like it is.

[pvanheus]

Coming to this late - pathogen-profiler is the underlying tool that tb-profiler uses. It depends on delly 1.2.6. The tb-profiler 4.6.0 in bioconda depends on pathogen-profiler 4.5.0 which has exactly this dependency (delly 1.2.6). I don't understand why an extra requirement is needed in the tool wrapper?

[bgruening]

Thanks @emarinier