Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
Hi Curtis,
This is a good question.
I'll post back to the list to (hopefully) gather some feedback.
Thanks!
Jen
On 8/25/11 8:44 AM, Robert Curtis Hendrickson wrote:
Wonderful. We're on galaxy-dist, but we can pull that patch. Are most local installs on Dist or Central?
Thanks!
Curtis
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Thursday, August 25, 2011 10:41 AM To: Robert Curtis Hendrickson Cc: David K Crossman; 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
Hi Curtis,
Changeset details: http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9
We are planning on releasing a distribution within a week, so alternatively you could wait and pull from there, if you normally work from the galaxy-dist repository.
And for everyone tracking this fix: the changeset was applied to the public Galaxy main instance yesterday (http://usegalaxy.org).
Hope this helps!
Jen Galaxy team
On 8/25/11 7:55 AM, Robert Curtis Hendrickson wrote:
Jen,
Can you also please describe the details of the fix? We need to fix the same issue in our local instance, but don't know if this
was a fix to cuffdiff, or to galaxy. Which one should we be updating?
Regards, Curtis
Hi,
We have a local instance of galaxy at our institution. I've been trying to use several existing wrappers for tools on galaxy right now, for example, bwa_wrapper, cufflinks_wrapper to run bwa, cufflinks through galaxy. I keep seeing the following error:
An error occurred running this job:Could not determine BWA version The alignment failed. Error aligning sequence. /bin/sh: bwa: not found
An error occurred running this job:Could not determine cufflinks version cufflinks -I 300000 -F 0.050000 -j 0.050000 -p 4 -Q 0 -r Error running cufflinks. /bin/sh: cufflinks: not found
This is despite the server having cufflinks and bwa available. Is there somewhere I need to put these executables? Any config/ini files that I need to update with the location of the executables?
Thanks for any help, Dhivya
dhivya arasappan wrote:
Hi,
We have a local instance of galaxy at our institution. I've been trying to use several existing wrappers for tools on galaxy right now, for example, bwa_wrapper, cufflinks_wrapper to run bwa, cufflinks through galaxy. I keep seeing the following error:
An error occurred running this job:Could not determine BWA version The alignment failed. Error aligning sequence. /bin/sh: bwa: not found
An error occurred running this job:Could not determine cufflinks version cufflinks -I 300000 -F 0.050000 -j 0.050000 -p 4 -Q 0 -r Error running cufflinks. /bin/sh: cufflinks: not found
This is despite the server having cufflinks and bwa available. Is there somewhere I need to put these executables? Any config/ini files that I need to update with the location of the executables?
Hi Dhivya,
If you log in as the user which runs the Galaxy process, is `bwa` available on the $PATH (e.g. on the command line w/o specifying a path).
Thanks, --nate
Thanks for any help, Dhivya
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dhivya arasappan -
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Nate Coraor