Hi,
Today I downloaded the new Galaxy version which supports python 2.6. I 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.
Sincerely,
Freerk van Dijk
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