On Mon, Nov 18, 2013 at 2:24 PM, Dave Bouvier email@example.com wrote:
It turns out there were two problems. First, the test environment was not resolving the upload tool's dependency on samtools, which I've now corrected.
On a closely related point, I understand Galaxy likes to store all BAM files co-ordinate sorted and indexed - when a tool produces a BAM file where does this happen? i.e. Is it the individual tool's responsibility, or the framework (e.g. during setting metadata). I am assume the later, in which case is there still an implicit samtools dependency there?
Second, the bam file detection on upload was broken due to the bug in python 2.7.4's gzip module, which I've also corrected.
You mean http://bugs.python.org/issue17666 fixed in 2.7.5?
I reported that when Biopython's BGZF support broke (BGZF being the gzip flavour used for BAM and tabix style indexed files).
I have re-run the test framework on samtools_idxstats, and it has now passed its test.
Thanks Dave :)