[galaxy-user] Galaxy test won't run a bwa job

Mike Dufault dufaultm at yahoo.com
Tue Nov 22 16:32:00 EST 2011


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

--- On Tue, 11/22/11, Carlos Borroto <carlos.borroto at gmail.com> wrote:

From: Carlos Borroto <carlos.borroto at gmail.com>
Subject: Re: [galaxy-user] Galaxy test won't run a bwa job
To: "Jennifer Jackson" <jen at bx.psu.edu>
Cc: galaxy-user at 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

On Tue, Nov 22, 2011 at 12:30 PM, Jennifer Jackson <jen at bx.psu.edu> 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
>
> On 11/22/11 7:56 AM, Carlos Borroto 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
>> ___________________________________________________________
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>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support
>

___________________________________________________________
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:

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