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
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