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.
On Wed, Jan 23, 2013 at 6:35 PM, Anthonius deBoer <thondeboer(a)me.com> wrote:
I also second this request to get it addressed (Where can we vote on
fixes ?! :) ...It is very weird that samtools is run on the local machine
and it even does the indexing sequentially...
On Jan 23, 2013, at 03:28 PM, Kyle Ellrott <kellrott(a)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
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
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