On Mon, Nov 18, 2013 at 2:24 PM, Dave Bouvier <d...@bx.psu.edu> wrote: > Peter, > > 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.
Excellent. 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. > > --Dave B. Thanks Dave :) Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/