[galaxy-user] Galaxy test won't run a bwa job
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 ___ 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/
Re: [galaxy-user] Galaxy test won't run a bwa job
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 ___ 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/ -- 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: http://lists.bx.psu.edu/
Re: [galaxy-user] Galaxy test won't run a bwa job
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 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 >> ___ >> 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/ > > -- > 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: http://lists.bx.psu.edu/
Re: [galaxy-user] Galaxy test won't run a bwa job
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 wrote: From: Carlos Borroto Subject: Re: [galaxy-user] Galaxy test won't run a bwa job To: "Jennifer Jackson" 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 On Tue, Nov 22, 2011 at 12:30 PM, Jennifer Jackson 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 >> ___ >> 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/ > > -- > 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: http://lists.bx.psu.edu/___ 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/
Re: [galaxy-user] Galaxy test won't run a bwa job
Thanks Mike, that's what I ended doing. On Tue, Nov 22, 2011 at 4:32 PM, Mike Dufault wrote: > 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 * wrote: > > > From: Carlos Borroto > Subject: Re: [galaxy-user] Galaxy test won't run a bwa job > To: "Jennifer Jackson" > 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 > > On Tue, Nov 22, 2011 at 12:30 PM, Jennifer Jackson > http://mc/compose?to=j...@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 > >> ___ > >> 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/ > > > > -- > > 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: > > http://lists.bx.psu.edu/ > > ___ 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/
