/usr/bin/picard Re: bcbio will need another while - needs gatk

[Steffen Möller <steffen_moeller@gmx.de>]

Hello,

I installed a binary distribution of gatk and then ran a bit into
trouble over

$ apt-file search /usr/bin/picard
picard: /usr/bin/picard
picard-tools: /usr/bin/picard-tools

I tend to think that this exposes a weakness of Debian - it misses
namespaces. Others may say that it is a strength. Don't think so. You
want to use the same scripts that your scientific peer uses. Everything
else goes under "the distribution has patches, the work may not be
completely reproducible" - because a log file has a different hash value
since executions of /usr/bin/picard were changed to /usr/bin/picard-tools.

At the moment the tests are a bit weird in that it fails over not
finding its configuration files

ValueError: Could not find input system configuration file
/tmp/bcbio_cl6jd4o1/test_automated_output/bcbio_system.yaml, including
inside standard directory /galaxy
steffen@wurzel:~/med/bcbio$ find . -name bcbio_system.yaml
./debian/bcbio/usr/share/bcbio/config/bcbio_system.yaml
./config/bcbio_system.yaml

but we are at

4 failed, 8 passed, 71 deselected, 47 warnings in 272.41 seconds

Should we have someone among us for who packaging go-based software
feels like easy then the newly surfaced https://github.com/brentp/gsort
would be nice.

And - qualimap. The jar files are still missing that we need to build that.

Also need to look at how picard is invoked since somehow this does not
seem compatible - or it is just because of version differences.

Steffen


On 12.11.20 22:02, Steffen Möller wrote:
> [2020-11-12T20:56Z] /usr/bin/bash: line 1: gatk: command not found
>
> There are also other issues, like use using a newer version of STAR
> (rna-star) and the file testing against is not prepared for that. Kind
> of neat: The hts-nim-tools should have an executable with hyphens, not
> underscores. Conda did this wrong but now bcbio adopted this. Upstream
> offered to change to underscore but I just added a symlink and would
> like to learn from this trivial case about the difficulties this makes
> and if this is also something that our link to bio.tools can help with.
>
> Let's see.
>
> Best,
>
> Steffen
>