On Tue, May 24, 2016 at 11:42 AM, Raymond Wan <rwan.w...@gmail.com> wrote:
> Hi Peter,
>
>
> On Tue, May 24, 2016 at 6:29 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> In case you didn't know, Galaxy likes to keep all BAM files in
>> coordinate sorted order with a BAI index (using samtools).
>> Somehow this is failing on your system (perhaps a suitable
>> version of samtools is not on the $PATH).
>
>
> No, I wasn't aware of this.  Actually, I was looking just now and
> galaxy/database/sw_dir/samtools/ looks like this:
>
> $ ls
> 0.1.16  0.1.18  0.1.19  1.1  1.2
>
> So, it seems like we have several versions installed.  (I don't know
> why -- I presume various tools pulled in different dependencies?  I
> didn't know it looked like this until I went searching.)

Galaxy has a complex tool dependency mechanism which allows for
user-facing tools to call a specific version of an installed command
line tool.

However, for the metadata processing, I believe Galaxy itself just
uses whichever samtools is on the $PATH (and ignores all the
clever Galaxy specific tool dependency stuff).

Peter
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