I'm willing to put in the coding time, but I'd need some pointers on the
best way to go about making the changes.

Kyle


On Wed, Jan 23, 2013 at 6:35 PM, Anthonius deBoer <thondeb...@me.com> wrote:

> I also second this request to get it addressed (Where can we vote on bug
> fixes ?! :) ...It is very weird that samtools is run on the local machine
> and it even does the indexing sequentially...
> Thon
>
>
> On Jan 23, 2013, at 03:28 PM, Kyle Ellrott <kellr...@soe.ucsc.edu> wrote:
>
> I'm currently in the process of loading (path paste) a large library of
> BAM files (>10000) into the shared Data Libraries of our local galaxy
> installation, but I'm finding this process to be very slow.
> I'm doing a path paste, and not actually copying the files. I have
> disabled local running of 'upload1', so that it will run on the cluster,
> and set 'set_metadata_externally' to true.
> It looks like the job handlers are calling 'samtools index' directly.
> Looking through the code, that seems to happen in galaxy/datatypes/binary
> in Bam.dataset_content_needs_grooming, where it calls 'samtools index' and
> then waits.
> What would be the most efficient way to start changing the code so that
> this process can be done by an external script, at a deferred time out on
> the cluster?
>
> Kyle
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