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.)

However, we have command-line access and /usr/bin/samtools *is* 0.1.18
.  I can get back to the user and ask him which tool he was using at
the time of the failure.  Is it difficult to "force" the version of
samtools that the tool uses?  I don't know how tools are installed,
but if it's a matter of editing XML files, then maybe we can do that.

> I'm sure a Galaxy expert can and will comment, but it looks like
> while trying to sort the BAM file in order to index it, something
> fails on the cluster side. This means the BAI index does not
> exist, so Galaxy cannot access the BAM file metadata. I'm
> still surprised if this is why Galaxy is not starting up - but
> perhaps you've found a new bug?

So the instance we are using is from January.  As the system is "in
production", we are reluctant to update it from Github.

Of course, this is preventing the system from starting so if a recent
update fixes this problem, we'll be more included to do a pull.

> If no one else has any suggestions and this is urgent, I would
> try manually sorting and indexing the problem BAM file(s) outside
> of Galaxy using samtools, and see if after that Galaxy can restart?

Ok -- that is worth considering.  Can I find the offending file, sort
it (via the command-line) and replace it?  I'm hesitant to do this
since I'm worried it will negatively affect the database (i.e.,
corrupting it, if it stores some kind of md5 signature of files).  But
if there is no harm, then we will give that a try.

Thanks for the suggestion!

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