Hi Steffen,
On Fri, Nov 13, 2020 at 10:25:39PM +0100, Steffen Möller wrote:
> 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.
We have the workaround
/usr/lib/debian-med/bin/
see for instance in eigensoft[1] and lots of other packages. Simply
provide this for picard-tools and make sure gatk users set the PATH
accordingly.
> 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.
Nilesh did so several times.
> And - qualimap. The jar files are still missing that we need to build that.
Simply ping the authors about this. As far as I remember the last
status was that sources are lost (?????) and a backup needs to be found.
> Also need to look at how picard is invoked since somehow this does not
> seem compatible - or it is just because of version differences.
See above for picard-tools. You might like to try this first.
Kind regards
Andreas.
[1]
https://salsa.debian.org/med-team/eigensoft/-/blob/master/debian/README.Debian
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