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Question: Galaxy Test Won'T Run A Bwa Job
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gravatar for Carlos Borroto
7.0 years ago by
Carlos Borroto • 390
Washington Metropolitan Area
Carlos Borroto • 390 wrote:
Hi, I'm trying to test a workflow using tools only available on the test server, for this I have uploaded a limited subset of my data that should run fairly quickly. The first step is a BWA mapping, but the job has being in the queue since yesterday. Is it fine to run this kind of test there? Thanks, Carlos
bwa alignment • 898 views
ADD COMMENT • link •
modified 7.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.0 years ago by Carlos Borroto • 390
0
gravatar for Jennifer Hillman Jackson
7.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Carlos, The NGS cluster was down yesterday for maintenance. Restarting the BWA job should initiate the run. Hopefully this helps, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k
Hi Jen, I did as you recommended a rerun my job, but after 2hrs is still waiting. This is my history if that helps: http://test.g2.bx.psu.edu/u/cjav/h/gatk---hg19---example Regards, Carlos
ADD REPLY • link written 7.0 years ago by Carlos Borroto • 390
Hi Carlos, You can always run your BWA on the Main Galaxy and then import the data directly into the Test Galaxy using the http: address; no need to download to your local machine. The http: address can be found by by selecting properties on the disk icon. Instead of downloading, you can just copy the http:. I hope this helps, Mike Subject: Re: [galaxy-user] Galaxy test won't run a bwa job To: "Jennifer Jackson" <jen@bx.psu.edu> Cc: galaxy-user@lists.bx.psu.edu Date: Tuesday, November 22, 2011, 3:12 PM Hi Jen, I did as you recommended a rerun my job, but after 2hrs is still waiting. This is my history if that helps: http://test.g2.bx.psu.edu/u/cjav/h/gatk---hg19---example Regards, Carlos ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:   http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at:   http://lists.bx.psu.edu/
ADD REPLY • link written 7.0 years ago by Mike Dufault • 270
Thanks Mike, that's what I ended doing.
ADD REPLY • link written 7.0 years ago by Carlos Borroto • 390
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