August 2012 - galaxy-user - lists.galaxyproject.org

Local instance and storage space to provide
by Scott McManus 03 Aug '12

03 Aug '12

Hi Sarah- Thanks for letting me post this to galaxy-user - I think it's a good question. You can purge deleted datasets by clicking on the cog in the righthand corner of the browser window. Clicking the cog should cause a list of actions to appear, including "Purge Deleted Datasets". You can also setup a cron job to use the scripts in galaxy's scripts/cleanup_datasets directory. -Scott ----- Original Message ----- > Hi Scott, > > Thanks a lot for these explanations. > > Tell me if I'm right, but when a use delete permaently a dataset, > this > dataset is kept in /database/files/000/dataset*, the deleted dataset > is > not purged. This is a porblem, is not it ? Or my local instance 's > configuration is not a good one. > > Thanks in advance, > Sarah >

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Lost my history!
by Jean-Philippe Couture 02 Aug '12

02 Aug '12

Hi, I went to the galaxy web page as usual this morning, but my history was no longer present! I'm not sure I was logged in (:-[ ), but every time i went on the galaxy web page, my history was there. Do you have any idea of what could've happen? Thanks a ton! -- Jean-Philippe Couture, Ph.D. Laboratoire du Dr. Nicolas Gévry, Université de Sherbrooke. Jean-Philippe.Couture(a)USherbrooke.ca

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Conservation (i.e. PhastCons) Q
by Vincent Joseph Lynch 02 Aug '12

02 Aug '12

Hi All, I am using Galaxy (main) and would like to intersect a bed file I have with the PhastCons scores (primarily placental and primate). After much searching around I can't tell if these files are locally cached and if so how I access them. Alternatively I could get them directly from UCSC, but it seems like these files would be rather large and useful to other users as well. (I apologize if I am missing the obvious, I'm still a novice user.) I am using hg19, but of course could lift over to convert the coordinates. Best, Vinn Vincent J. Lynch, Ph.D. Associate Research Scientist Department of Ecology and Evolutionary Biology (EEB) & Yale Systems Biology Institute (YSBI) Yale University "There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." -C. Darwin, 1859

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Fwd: PBS Server Throwing Errors
by Scott McManus 02 Aug '12

02 Aug '12

This has been forwarded from galaxy-dev. -Scott ----- Forwarded Message ----- From: "Scott McManus" <scottmcmanus(a)gatech.edu> To: "Daniel Patrick Sullivan" <dansullivan(a)gmail.com> Cc: galaxy-dev(a)lists.bx.psu.edu Sent: Wednesday, August 1, 2012 4:46:26 PM Subject: Re: [galaxy-dev] PBS Server Throwing Errors Hi Dan- Thanks again for your great hospitality at UCI! It looks like you've done most of the sane things, and a quick check looks like the PBS egg is requesting protocol version 1 while the server supports protocol version 2. One possibility is that there is a protocol mismatch, which could be the result of using an old library. We can check if the egg is at fault first - try the following link for compiling the pbs_python.py egg yourself and try the example to see if the connection and a simple stats-gathering operation (the examples/pbsnodes-a.py script from pbs_python) works: https://subtrac.sara.nl/oss/pbs_python/wiki/TorqueInstallation -Scott ----- Original Message ----- > Hi, Galaxy Community, > > Greetings from The University of Chicago; I hope all who attended the > Galaxy conference enjoyed it as much as I did. I have searched the > mailing list archives as well as Google to a resolve problem I am > seeing, however I am somewhat at a loss as to the next course of > action I should be taking to bring this issue to a close. I am > hoping > that one of the bright minds on this mailing list could help me shed > some light on the solution to my problem, or at least help me > identify > a root cause. I have configured Galaxy to integrate with TORQUE > (version 4.0.2) server, and successfully built the PBS python egg as > specified in the Galaxy documentation. I am using Python version 2.6 > and the latest build of Galaxy. Whenever I launch a job from the > Galaxy UI, I get the following error message(s) on the PBS server: > > 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting > version numbers, 1 detected, 2 expected > 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply > code=15058(Bad DIS based Request Protocol MSG=cannot decode message), > aux=0, type=AlternateUserAuthentication, from galaxy@ > 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting > version numbers, 1 detected, 2 expected > 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply > code=15058(Bad DIS based Request Protocol MSG=cannot decode message), > aux=0, type=QueueJob, from galaxy@ > 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting > version numbers, 1 detected, 2 expected > 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply > code=15058(Bad DIS based Request Protocol MSG=cannot decode message), > aux=0, type=Disconnect, from galaxy@ > 07/30/2012 15:43:01;0002;PBS_Server;Svr;PBS_Server;Torque Server > Version = 4.0.2, loglevel = 1 > > One thing I did notice, that suggests there might be a problem, is > that there is no hostname after the galaxy@; most of the other > messages in this log file have a host name appended to log entry, > i.e.: > > 07/30/2012 15:43:38;0100;PBS_Server;Req;;Type StatusJob request > received from root@sc01, sock=10 > > I have completed a tcpdump on the schedule node, and I can definitely > see bi-directional traffic between the Galaxy server and the > scheduler > node on TCP port 15001. In addition to this, I have installed the > TORQUE client tools on on the Galaxy server, and can spawn an > interactive job with qsub -I, as well as check the status of queued > jobs using qstat (from the Galaxy server). This suggests to me that > there a potential problem with the PBS Egg, although I am not > certain. > Has anybody seen something like this before, or could somebody point > me in the right direction? We do have a support contract with > Adaptive Computing, and I am opening a ticket with them as well, > however I wanted to reach out to the Galaxy community to cover all of > my bases. Thank-you so much for taking the time to read my email. > > Dan Sullivan > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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Fwd: [galaxy-dev] Local instance and storage space to provide
by Scott McManus 02 Aug '12

02 Aug '12

I'm forwarding this to galaxy-user instead of galaxy-dev. -Scott ----- Forwarded Message ----- From: "Scott McManus" <scottmcmanus(a)gatech.edu> To: "Sarah Maman" <sarah.maman(a)toulouse.inra.fr> Cc: galaxy-dev(a)lists.bx.psu.edu Sent: Wednesday, August 1, 2012 4:18:29 PM Subject: Re: [galaxy-dev] Local instance and storage space to provide Hi Sarah- I'm sure others have experiences that could help, so I hope they will chime in. Nate put together some slides two years ago on production setups, including some architecture for the server main.g2.bx.psu.edu: http://wiki.g2.bx.psu.edu/Events/GDC2010?action=AttachFile&do=get&target=GD… There is also a wiki page describing production environments: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server Again, I'm sure others have had different experiences with both more and less hardware on hand. Of course your mileage may vary based on the tools being used (which in your case I'm guessing is Tophat), the number of datasets that will need to be analyzed, and so on. I hope that helps! -Scott ----- Original Message ----- > Dear all, > > To purchase equipment related to a local instance of Galaxy, I would > like to have your feedback. > > Did you notice load problems when 10 to 20 users launch jobs at the > same > time and on a single instance of Galaxy, with mi-RNA or RNA seq data > ? > > What do you recommend in terms of storage space, number of nodes, > number > of instances? > > Thank you in advance, > Sarah Maman > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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Running Cufflinks on Bacterial RNAseq data
by Rachel Krasich 01 Aug '12

01 Aug '12

I am attempting to run Cufflinks on Galaxy main to analyze my E. coli RNAseq data. I have mapped my reads using an outside program (Genious) and uploaded the resulting BAM file. I also have uploaded the E. coli annotations as a gtf file. However when I attempt to run Cufflinks using my annotations it just stays on "Job is waiting to run" for hours. If I click on "Edit attributes", I see an error message "Required metadata values are missing". Does this mean that my files are somehow incomplete and cufflinks will never run, or do I just need to wait longer? When searching around the mailing lists I saw others have had issues with bacteria due to its circular chromosome, and was wondering if this might somehow be related. Thanks. Rachel

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SNP analysis in Galaxy
by shamsher jagat 01 Aug '12

01 Aug '12

I posted this question in Dev- list so re-posting to correct list with some additional information. I have paired end sequencing files on which I would like to call SNPs compared to databases well check sequence variation among samples. I dont have access to any local galaxy instance. My question are- 1. Is there a way that I can upload these large files to galaxy and analyze them then delete? 2. Is there a work flow to call SNPs and analyze and annotate SNPS in Galaxy, If some one know about a work flow summarized by some one in addition to Galaxy list that will be bonus. Thanks Kanwar

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Datasets permanently deleted
by Sarah Maman 01 Aug '12

01 Aug '12

Dear all, In the menu "User" -> "Saved Datasets", all datasets are listed even if some of them have been deleted permanently by deleting its history. So, it's possible to copy an deleted dataset in the current history and that is confusing for users. Do you have any solution to drop these datasets in "saved datasets" ? Thanks in advance, Sarah Maman

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