Re: [galaxy-user] History items remain pending (grey color)
Hi Priya, If you are using one of the public Galaxy servers (e.g. http://main.g2.bx.psu.edu/), then it's quite probable that there a lots of jobs queued in the system by other users. If your history item is grey that means the job has been successfully submitted and is waiting its turn in the queueing system. When the system is busy it will take longer for the jobs to be submitted due to the high demand. In short - give it some time, it will run eventually. Best wishes, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 25/03/2013 23:01, Priya Bhatt priya.bh...@loni.ucla.edu wrote: Dear Galaxy Users, Forgive me in advance, but I am a VERY new Galaxy user! I am trying to go through the Galaxy 101 tutorial provided on the galaxy website (https://main.g2.bx.psu.edu/u/aun1/p/galaxy101). The first step asks to get exon data of Chromosome 22 from UCSC database, and the second step asks to get the SNP data from the same database. When I do these two steps, I understand the history items should turn green once they are processed, however after a few hours these items remain grey. Am I doing something wrong? Any help would be greatly appreciated! Thank you in advance, Priya ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] [Gmod-gbrowse] Last day for early registration for GMOD 2013
GMOD is very pleased to announce the keynote speaker for the 2013 GMOD community meeting is Dr. Kentaro Yoshida from the Sainsbury Lab ( http://tsl.ac.uk), talking about the Open Ash Dieback effort. This pioneering bioinformatics project is employing two increasingly important paradigms--open access to data and crowdsourcing--to gather genetic analyses of ash and a fungal pathogen that is threatening tree populations in the UK. Expect an interesting and inspiring talk! Online registration: http://gmod2013.eventbrite.com If you are interested in attending remotely, we will be using Go To Meeting (http://gotomeeting.com) to allow people to attend virtually. Please email me if you would like to join in. Look forward to seeing you all in Cambridge! On Wed, Mar 20, 2013 at 7:28 PM, Scott Cain sc...@scottcain.net wrote: Hi, With several guest speakers, including Jane Lomax from GO, Joseph Rossetto from the EBI, and Manuel Corpas from the Genome Analysis Centre, this GMOD meeting is shaping up to be a very intersting meeting indeed. Today (March 21) is the last day to register with the early registration pricing. To register, go to http://gmod2013.eventbrite.com/ I look forward to seeing you next month (April 5-6) in Cambridge, England. For more information about GMOD 2013, go to http://www.gmod.org/wiki/April_2013_GMOD_Meeting Scott -- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ Gmod-gbrowse mailing list gmod-gbro...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Amelia Ireland GMOD Community Support http://gmod.org || @gmodproject ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] hello Newbie questions about galaxy and clustering
hello I have installed an galaxy instance for purpose testing on a 8 CPU server without problem all run perfectly. I have made some galaxy xml wrapper to understant how galaxy calls program and other little things. Now I want to install a Galaxy server with a cluster configuration. Before I have tested HTCondor but I have no Idea how I can mix Galaxy and HTCondor. The perfect thing was somebody have already tested this type of condor. But I can satisfy myself with any other cluster type. What I don't understant in fact ( maybe my worst problem ) where lie all parts of this puzzle. I explain. I know that I need Galaxy. I know too I need a cluster ( in my case HTCondor ) I understand I need something between these 2 parts ... I think something like PBS or SGE but it's not totaly clear for me I'm search on galaxy mailling list archive ... but I just found 2 mails in 2008 :( has anybody made this conf or have a configuration ? greetings PS : sorry for my poor english :) ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Could not find the refseq from database list
Hi Xiaogeng, Your genome can be loaded in .fasta format into a dataset and used as a custom reference genome. Annotation files can also be loaded as a dataset. Once loaded, both will then be available to use with tools, along with your loaded sequence data. Help with loading: http://wiki.galaxyproject.org/Support#Trouble_loading_data Help for Custom Genomes: http://wiki.galaxyproject.org/Support#Custom_reference_genome Best, Jen Galaxy team On 3/25/13 7:31 PM, xiaogeng Feng wrote: Hi, I am using Galaxy to analyze Chlamydia trachomatis F/SW4 illumina sequence. We could not find this genome in your dataset list. Is there a way to import Chlamydia trachomatis F/SW4 sequence to Galaxy? how about the annotation file? Many thanks, Xiaogeng ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] History items remain pending (grey color)
Hello Priya, Graham is correct in stating that a "grey dataset" indicates that the job is still in the queue waiting to run. When the public server is very busy, this delay can vary based on a few factors, but a UCSC Table Browser data extraction is not a job that would be expected to take very long. That said, the public server was known to be slower later yesterday through this morning. We are actively working to resolve this and you should notice improvement shortly. I was able to get a small test job through (also a UCSC Table data extraction) even during this time - with some delay, but not on the order of several hours. Have your jobs completed now and were you able to work through the exercise since first reporting the issue? If jobs were stalled, please try again one more time and if there is problem that continues through this afternoon, please let us know. The exercise was designed to not be computationally intensive - and you should be able to complete it during a single work session. Just to let you know, sometimes it appears that jobs are waiting, when actually all that is needed is a "History refresh" to update the panel to show the current status. I've misinterpreted status myself by forgetting to do this on occasion (still!). A manual refresh certainly isn't always needed, but is worth knowing about. There is a small double-arrow rounded icon at the top of the History panel, to the left of the gear icon, that you can click to do the refresh, here is a picture of it: Hopefully this helps, Jen Galaxy team On 3/25/13 4:01 PM, Priya Bhatt wrote: Dear Galaxy Users, Forgive me in advance, but I am a VERY new Galaxy user! I am trying to go through the Galaxy 101 tutorial provided on the galaxy website (https://main.g2.bx.psu.edu/u/aun1/p/galaxy101). The first step asks to get exon data of Chromosome 22 from UCSC database, and the second step asks to get the SNP data from the same database. When I do these two steps, I understand the history items should turn green once they are processed, however after a few hours these items remain grey. Am I doing something wrong? Any help would be greatly appreciated! Thank you in advance, Priya ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] History items remain pending (grey color)
Dear All, Thank you for your prompt responses. Yes, my jobs have processed - I guess I needed to be more patient! As far as the tutorial, it was taking much time on the version available to the public on the Galaxy website but I am now using an instance of Galaxy on my lab's network so things are moving almost instantaneously. Thanks for your insight! Best, Priya From: Jennifer Jackson [j...@bx.psu.edu] Sent: Tuesday, March 26, 2013 12:14 PM To: Priya Bhatt Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] History items remain pending (grey color) Hello Priya, Graham is correct in stating that a grey dataset indicates that the job is still in the queue waiting to run. When the public server is very busy, this delay can vary based on a few factors, but a UCSC Table Browser data extraction is not a job that would be expected to take very long. That said, the public server was known to be slower later yesterday through this morning. We are actively working to resolve this and you should notice improvement shortly. I was able to get a small test job through (also a UCSC Table data extraction) even during this time - with some delay, but not on the order of several hours. Have your jobs completed now and were you able to work through the exercise since first reporting the issue? If jobs were stalled, please try again one more time and if there is problem that continues through this afternoon, please let us know. The exercise was designed to not be computationally intensive - and you should be able to complete it during a single work session. Just to let you know, sometimes it appears that jobs are waiting, when actually all that is needed is a History refresh to update the panel to show the current status. I've misinterpreted status myself by forgetting to do this on occasion (still!). A manual refresh certainly isn't always needed, but is worth knowing about. There is a small double-arrow rounded icon at the top of the History panel, to the left of the gear icon, that you can click to do the refresh, here is a picture of it: [cid:part1.08040502.09070800@bx.psu.edu] Hopefully this helps, Jen Galaxy team On 3/25/13 4:01 PM, Priya Bhatt wrote: Dear Galaxy Users, Forgive me in advance, but I am a VERY new Galaxy user! I am trying to go through the Galaxy 101 tutorial provided on the galaxy website (https://main.g2.bx.psu.edu/u/aun1/p/galaxy101). The first step asks to get exon data of Chromosome 22 from UCSC database, and the second step asks to get the SNP data from the same database. When I do these two steps, I understand the history items should turn green once they are processed, however after a few hours these items remain grey. Am I doing something wrong? Any help would be greatly appreciated! Thank you in advance, Priya ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
