So it wasn't in 15.01 - it was before that but the local job runner
was changed to set metadata as part of the job (I think probably
sometime in 2014). When it was setting metadata externally it might
have used slightly different dependency resolution strategies that
would result in samtools being
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
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
