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 >