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
” 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
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
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
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
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
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
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
)
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,
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
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