[galaxy-dev] BWA error post upgrade - local galaxy

2012-11-07 Thread Kelkar, Hemant
We recently upgraded our local galaxy install and followed the procedure that now uses "bwa" from the galaxy toolshed. Since the upgrade "bwa" alignments are generating the following error (exact file paths redacted): [bwt_restore_bwt] fail to open file '/path_to/bwa_path/mm9_all.fa.rbwt'. Abort

Re: [galaxy-dev] possible to resume failed workflow?

2012-05-25 Thread Kelkar, Hemant
” jobs. --Hemant From: J. Greenbaum [mailto:jgb...@liai.org] Sent: Friday, May 25, 2012 11:42 AM To: Kelkar, Hemant Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] possible to resume failed workflow? Hi Hermant, Thanks for the suggestion. I've tried setting that parameter to 5, but i

Re: [galaxy-dev] possible to resume failed workflow?

2012-05-25 Thread Kelkar, Hemant
Jason, Are the affected workflow steps actually failing or are they falsely being reported as “failed” (have you checked if correct output exists for the affected step)? Once a step/job is marked “failed’ you can’t use the output (even if it exists) for any subsequent step. If you are using a

Re: [galaxy-dev] http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway

2012-05-25 Thread Kelkar, Hemant
Working fine as of now. --hk -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock Sent: Friday, May 25, 2012 6:09 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] http://toolshed.g2.bx.psu.edu/ 502 Bad G

Re: [galaxy-dev] Uploading problem

2012-05-22 Thread Kelkar, Hemant
Are these problems cropping up because of possible system resource limits being imposed on the user that is running galaxy? It may be worthwhile to check the /etc/login.conf (not sure that the analogous file is in Ubuntu). Same may be true for Postgres (http://www.postgresql.org/docs/8.2/static

Re: [galaxy-dev] Problem related to a job that "failed"

2012-05-14 Thread Kelkar, Hemant
Increasing the 'retry_job_output_collection' value in universe_wsgi.ini fixed the "failed" job problem. Thanks for the suggestion Nate. --Hemant -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Friday, May 11, 2012 3:54 PM To: Kelkar, H

Re: [galaxy-dev] Problem related to a job that "failed"

2012-05-11 Thread Kelkar, Hemant
ter" as you had suggested first to see if we can avoid the "failed" job problem altogether. Thanks again. -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Friday, May 11, 2012 4:20 PM To: Kelkar, Hemant Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy

Re: [galaxy-dev] Problem related to a job that "failed"

2012-05-11 Thread Kelkar, Hemant
No I did not execute it on the "galaxy" server. I do not have shell access to the blade that actually runs the galaxy server. So I would need to get my sys admin to run this then? >That's pretty odd, you're executing this on the Galaxy server? What happens >if you run fetch_eggs.py in the sam

Re: [galaxy-dev] Problem related to a job that "failed"

2012-05-11 Thread Kelkar, Hemant
) galaxy.eggs.EggNotFetchable: ['Cheetah'] -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Friday, May 11, 2012 3:54 PM To: Kelkar, Hemant Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem related to a job that "failed" On May 11,

[galaxy-dev] Problem related to a job that "failed"

2012-05-11 Thread Kelkar, Hemant
All, This question pertains to a local galaxy install where the jobs are being submitted to a cluster running LSF. I periodically get an error from a galaxy job ("Job output not returned from cluster") even though the job completes properly on the cluster. In researching this issue our syst