On Tue, May 24, 2016 at 11:42 AM, Raymond Wan <rwan.work@gmail.com> wrote:
Hi Peter,
On Tue, May 24, 2016 at 6:29 PM, Peter Cock <p.j.a.cock@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