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.
hmm, no replies yet, so is anybody able to reproduce this behavior
would you not consider it a bug?
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.
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> To search Galaxy mailing lists use the unified search at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: