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 De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Dijk, F van wrote:
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.
Hi Freerk, 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? Thanks, --nate
Freerk: Another question: which version of bowtie do you use? a. On Nov 26, 2009, at 11:14 AM, Dijk, F van wrote:
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
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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participants (3)
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Anton Nekrutenko -
Dijk, F van -
Nate Coraor