Re: [galaxy-user] User's information
On Friday, November 30, 2012, Sachit Adhikari wrote: Where are the user's information stored in Galaxy? I can't find the information in universe_wsgi. Regards, Sachit It is in the database (PostgreSQL usually, but MySQL is also supported, and for simple test setups even SQLite mostly works). The users' files are all on disk (with the extension .dat regardless of the file type). Peter ___ 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] Cuffdiff tracking file does not report all genes and trancrips from reference annotation?
Hello Wei, The results do sound strange. The best advice to start with is to make sure that you are up-to-date with both Galaxy and the RNA-seq tools and using the best possible inputs. 1 . Make sure that you are running the latest distribution http://wiki.galaxyproject.org/DevNewsBriefs 2. Update to use the current version of CuffDiff http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies 3. Use the iGenomes GTF annotation to make full use of the functionality in Cuffdiff http://cufflinks.cbcb.umd.edu/igenomes.html A good test to see if your set-up is correct would be to run the RNA-seq tutorial locally as a test case. http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise The reverse can also be done, if you have a problem locally, try running it as a small test (that still demonstrates the issue) on the Public Main server and see if the results can be duplicated. This can help determine if problem is with data inputs/settings or a problem with tool set-up/installation. It can also be a way to share your data with us if you need feedback. But, hopefully after updating the issue clears up! Jen Galaxy team On 11/29/12 11:51 AM, Wei Liao wrote: Hi, Galaxy user. I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to check differential expressed genes in my samples. I have 3 normals and 6 cancers samples, I did the following: - After tophat for each samples, run cufflink with refseq annotation which has 25266 genes and 43091 transcripts - cuffmerge all cufflink outputs contains 58112 lines - run cuffdiff with 3 normals as triplicate and compare to each cancer sample. Suprisingly, I fould out that the tanscripts tracking file, gene tracking, CDS tracking only has 2000 genes and 4000 transcripts. So the cufflink only compare 2000 genes and 4000 transcripts between samples. The question I want to ask here is that *why are the rest of the genes and transcripts not being tested and included in the tracking files?* Do you know what cause this kind of problem? Thanks, Wei -- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645 ___ 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/
[galaxy-user] December 2012 Galaxy Update
Hello all, The December 2012 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12at http://wiki.galaxyproject.org/GalaxyUpdates/2012_12. *Highlights:* - 37 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Papers, including papers on Trackster and CloudMan - Two new public Galaxy Servershttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Public_Galaxy_Servers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Who.27s_Hiringat seven different institutions - Upcoming Events and Deadlineshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Upcoming_Events_and_Deadlines - Source Code Documentationhttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Source_Code_Documentationis now available - New Galaxy Distributionhttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Galaxy_Distributions - New Galaxy CloudMan Releasehttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Galaxy_CloudMan_Release - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Other_News If you have anything you would like to see in the January *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Thanks, Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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] Analysis in queue but not running
Hi Lew, CC'ing the galaxy-user list because I am assuming that your question is about the free public server (Main) @ usegalaxy.org / main.g2.bx.psu.edu. If you have any future questions about Main, please post them to Galaxy-User so that others can see the question and respond. If I am reading the qstat output correctly, there are currently ~140+ jobs in the NGS queue, which means that Main is currently under very heavy load. The best thing to do is let the jobs sit in the queue. Killing and restarting them bumps them to the end of the queue. We are currently discussing a number of options for letting users know in situations like this, that while the job is not currently running, it is in the queue, and is moving forward. Thanks, Dave C PS: and the number of jobs in the queue has dropped by 2 since I started typing this email. On Fri, Nov 30, 2012 at 10:05 AM, Lewis Bowman lbow...@mailbox.sc.eduwrote: I have tried repeatedly to run Cuffdiff using cuffmerge output (38) and cufflinks output (25 and 29). In every case the job does not begin to run and status saysJob is waiting to run. Has Galaxy been down for the last several days? I am unsure what to do since I have received no error message. Thanks for you help. Lew Bowman -- Lewis H. Bowman Department of Biological Sciences University of South Carolina Columbia, SC 29208 PH: 803-777-5157 FAX: 803-777-4002 EMAIL: lbow...@mailbox.sc.edu -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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] dataset not visible
Hello Ilse, Your history/dataset issue was linked to a display problem that has now been resolved on the public Main Galaxy server. We found that this UI behavior was often linked to the use of Internet Explorer as a browser. For the best UI functionality when using Galaxy, we recommend using Firefox, Chrome, or Safari. Thank you for reporting the problem, Jen Galaxy team On 11/29/12 12:08 AM, Ilse Vandecandelaere wrote: Dear, I am working on the free public server of Galaxy for almost a week. When I opened the galaxy server this morning, my datasets were not visible. I have tried show hidden datasets or show deleted datasets, but nothing changed. How can I make my datasets visible? Thanks, Kind regards, Ilse --- http://www.ugent.be/fw/en/research/pharmaceutical-analysis/pmicro http://www.sociomicrobiology.ugent.be/ - ___ 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/
