Dijk, F van wrote:
Today I downloaded the new Galaxy version which supports python 2.6.
installed it and it works fine so far. But I'm experiencing some
problems with the speed of Galaxy compared to the version I was using
before. I perform alignments with Bowtie and for some reason it takes a
lot of time to go further with my workflows. I thought maybe it was due
to Bowtie using only 4 threads, so I changed the --threads option in
bowtie_wrapper.xml to 16 and performed the alignment again. When I take
a look at my processes I see Bowtie using 16 cores, but afterwards it
changes back to only using 4 cores while Galaxy (graphic webbrowser
view) still indicates it is busy with the alignment. This takes more
than 30 minutes, which it doesn't take with the older version. Do you
know how this is possible? Are there more settings which should/could be
changed to speed Galaxy up? I hope to hear from you soon.
So I understand the issue, if you instruct bowtie to use 16 cores, it
does initially and then (in the same job run) switches back to 4?