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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