Hi Wolfgang,

I only can tell you that we also have problems with handling BAM files properly in Galaxy. Our issue is more due to unsorted BAM files, but as far as I understood this is because the metadata creation changed from using samtools to using pysam. Maybe this helps you in finding a workaround.


Ciao,
Bjoern


hmm, no replies yet, so is anybody able to reproduce this behavior and would you not consider it a bug?

Best,
Wolfgang


On 06/16/2015 03:11 PM, Wolfgang Maier wrote:
Dear all,

with older Galaxies (prior to latest_15.03 I think), you could satisfy
Galaxy's samtools dependence for indexing bam files by having a samtools
executable in tool-dependencies/samtools/default/bin (with the
tool-dependencies directory declared as tool_dependency_dir in
galaxy.ini of course).

Now (checked with latest_15.03 and .05), this is not working any more!
The executable will still be used during bam uploads, but not when a bam
file gets created by a tool.

The reason is that before the job runner (tested this with the local job
runner only) used to build the dependency shell command for dependency
'samtools' before finishing a job, but now the job wrapper finish method
fails because it naively expects to find samtools on $PATH.

Best,
Wolfgang

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