Re: [galaxy-user] "Jobs is waiting to run" all day on Main
Thanks Jen. Yes, there is a format problem in my sequence file. The identifier was like "aaa.abc.contig1". After I deleted the first same letters to "contig1", then it could be added to custom build. Mengmeng - Original Message - From: "Jennifer Jackson" To: "Mengmeng Lu" Cc: galaxy-u...@bx.psu.edu Sent: Tuesday, July 24, 2012 2:14:56 PM Subject: Re: [galaxy-user] "Jobs is waiting to run" all day on Main Hello Mengmeng, I apologize for misunderstanding your original question. The problem is loading a dataset already in the history into the "Custom Builds" group. Either through the "User -> Custom Builds" or "Visualization -> Add Custom Build" link. First, double check your fasta dataset against the custom genome criteria: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome http://wiki.g2.bx.psu.edu/Learn/CustomGenomes Correct if necessary (troubleshooting help is also on wiki) and restart. If you are using one of the len file options, double check format against the file descriptions on the Custom Builds form itself. If you are still stuck, please share a copy of your history. Do this directly using "Options -> Share or Publish", add me as a share user "j...@bx.psu.edu", and email back when ready. Thanks, Jen Galaxy team On 7/24/12 7:55 AM, Lu, Mengmeng wrote: > Hi Galaxy team, > > I tried to "add a custom build" again yesterday. Till now, it has been in the > status of "processing" for almost one day. > > PS: I am using the public server. > > So is there anything wrong with my "new build"? > > Thanks. > > Mengmeng > > ----- Original Message ----- > From: "Jennifer Jackson" > To: "Mengmeng Lu" > Cc: galaxy-u...@bx.psu.edu > Sent: Monday, July 23, 2012 1:48:35 PM > Subject: Re: [galaxy-user] "Jobs is waiting to run" all day on Main > > Hello Mengmeng, > > Please try your upload process again and let us know if you continue to > have problems. > > Thank you! > > Jen > Galaxy team > > On 7/22/12 12:46 PM, Lu, Mengmeng wrote: >> Same problem here. >> >> I want to add a custom build, but it has been processing for more than 5 >> hours. Is it normal? >> >> PS: my reference genome which I used to add the custom build is about 42Mb. >> >> Thank you. >> >> Mengmeng >> > -- Jennifer Jackson http://galaxyproject.org ___ 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] "Jobs is waiting to run" all day on Main
Hi Galaxy team, I tried to "add a custom build" again yesterday. Till now, it has been in the status of "processing" for almost one day. PS: I am using the public server. So is there anything wrong with my "new build"? Thanks. Mengmeng - Original Message - From: "Jennifer Jackson" To: "Mengmeng Lu" Cc: galaxy-u...@bx.psu.edu Sent: Monday, July 23, 2012 1:48:35 PM Subject: Re: [galaxy-user] "Jobs is waiting to run" all day on Main Hello Mengmeng, Please try your upload process again and let us know if you continue to have problems. Thank you! Jen Galaxy team On 7/22/12 12:46 PM, Lu, Mengmeng wrote: > Same problem here. > > I want to add a custom build, but it has been processing for more than 5 > hours. Is it normal? > > PS: my reference genome which I used to add the custom build is about 42Mb. > > Thank you. > > Mengmeng > -- Jennifer Jackson http://galaxyproject.org ___ 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] "Jobs is waiting to run" all day on Main
Hello Mengmeng, I apologize for misunderstanding your original question. The problem is loading a dataset already in the history into the "Custom Builds" group. Either through the "User -> Custom Builds" or "Visualization -> Add Custom Build" link. First, double check your fasta dataset against the custom genome criteria: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome http://wiki.g2.bx.psu.edu/Learn/CustomGenomes Correct if necessary (troubleshooting help is also on wiki) and restart. If you are using one of the len file options, double check format against the file descriptions on the Custom Builds form itself. If you are still stuck, please share a copy of your history. Do this directly using "Options -> Share or Publish", add me as a share user "j...@bx.psu.edu", and email back when ready. Thanks, Jen Galaxy team On 7/24/12 7:55 AM, Lu, Mengmeng wrote: Hi Galaxy team, I tried to "add a custom build" again yesterday. Till now, it has been in the status of "processing" for almost one day. PS: I am using the public server. So is there anything wrong with my "new build"? Thanks. Mengmeng - Original Message - From: "Jennifer Jackson" To: "Mengmeng Lu" Cc: galaxy-u...@bx.psu.edu Sent: Monday, July 23, 2012 1:48:35 PM Subject: Re: [galaxy-user] "Jobs is waiting to run" all day on Main Hello Mengmeng, Please try your upload process again and let us know if you continue to have problems. Thank you! Jen Galaxy team On 7/22/12 12:46 PM, Lu, Mengmeng wrote: Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS: my reference genome which I used to add the custom build is about 42Mb. Thank you. Mengmeng -- Jennifer Jackson http://galaxyproject.org ___ 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] "Jobs is waiting to run" all day on Main
Hello Lee, When Galaxy is busy, the grey 'waiting to run' states means that the job is in the queue. You want to be sure to not delete/restart queued jobs or they move back to the end. Queue wait times can vary. It appears that your jobs have completed (there are none in the largest queue at this time). If you work is urgent, a cloud instance is the recommended alternative: http://usegalaxy.org/cloud Thank you! Jen Galaxy team On 7/21/12 3:20 PM, Lee Silver wrote: Since earlier today (at least 6 hours), all of my jobs have been stuck in the "waiting to run" state on the Main Galaxy server. Lee Silver (leemsil...@genepeeks.com) ___ 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://galaxyproject.org ___ 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] "Jobs is waiting to run" all day on Main
Hello Mengmeng, Please try your upload process again and let us know if you continue to have problems. Thank you! Jen Galaxy team On 7/22/12 12:46 PM, Lu, Mengmeng wrote: Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS: my reference genome which I used to add the custom build is about 42Mb. Thank you. Mengmeng -- Jennifer Jackson http://galaxyproject.org ___ 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] "Jobs is waiting to run" all day on Main
Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS: my reference genome which I used to add the custom build is about 42Mb. Thank you. Mengmeng - Original Message - From: "Mengmeng Lu" To: "Lee Silver" Sent: Sunday, July 22, 2012 2:45:52 PM Subject: Re: [galaxy-user] "Jobs is waiting to run" all day on Main Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS: my reference genome which I used to add the custom build is about 42Mb. Thank you. Mengmeng - Original Message - From: "Lee Silver" To: galaxy-u...@bx.psu.edu Cc: "Lee Silver" Sent: Saturday, July 21, 2012 5:20:19 PM Subject: [galaxy-user] "Jobs is waiting to run" all day on Main Since earlier today (at least 6 hours), all of my jobs have been stuck in the "waiting to run" state on the Main Galaxy server. Lee Silver (leemsil...@genepeeks.com) ___ 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/
