Re: [galaxy-user] Cistrome
Hello Albena, The Cistrome team should be contacted directly at: http://cistrome.org/ cistrome-b...@jimmy.harvard.edu Thanks, Jen Galaxy team On 10/25/11 5:08 PM, Albena Pramatarova, Dr wrote: Hi What is the procedure for getting a username and password key to use the Aspera tool? Thank you for your help. Albena ___ 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] Over disk quota
GANDRILLON OLIVIER wrote: Hello I just received the following message while using Galaxy through the web You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. I deleted a couple of files but it didn't helped. I checked the FAQ and could not get the answer. Hi Olivier, The FAQ page is out of date and we'll be updating this as soon as possible. Please see the following for information about how to free up disk space: http://wiki.g2.bx.psu.edu/Main http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets Sorry for the inconvenience, and thanks for using Galaxy. --nate Thank's for your help Olivier ___ 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] Names for genes in RNA-Seq analysis
Dear Carl After having solved a couple of other problems, I am now to the point where I can: 1.either get the FKPM and no names or 2. have the names and FKPM values to zero (or OK ?) So I was wondering whether you had solved this FKPM value problem with chicken you had? Best Olivier Le 26/10/11 02:21, « Jennifer Jackson » j...@bx.psu.edu a écrit : Hello Carl, Your question is similar to Olivier's, even though the problem is presenting in a different way. There is most likely a data mismatch problem as explained in my earlier reply to this thread and this prior mailing list question: http://gmod.827538.n3.nabble.com/Cufflinks-reporting-FPKM-values-of-all-ze roes-0-tt3183517.html#a3183928 Best wishes for your project as well, Jen Galaxy team On 10/20/11 7:32 AM, Carl Schmidt wrote: I am also using Galaxy to analyze RNA-seq libraries from chicken. While the names of the genes appear in the Cufflinks output, the FPKM values are all zero. On Oct 20, 2011, at 9:12 AM, GANDRILLON OLIVIER wrote: Hello I am using Galaxy to analyse RNA-seq libraries made from chicken cells. I just groomed my sequences, passed them through TopHat and then Cufflinks. This worked well and in the end I get a list of genes and their respective FPKM values. My only problem is that the names of the genes do not appears in the listing, they are simply reference as CUFF.1, CUFF.2, etcŠ Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer). Sincerely Olivier - New mail adress: olivier.gandril...@univ-lyon1.fr mailto:olivier.gandril...@univ-lyon1.fr Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33lang=en http://cgphimc.univ-lyon1.fr/spip.php?rubrique33lang=en Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux Tobie Nathan, in Qui a tué Arlozoroff ___ 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/ Carl Schmidt Associate Professor Animal Food Sciences University of Delaware Newark, DE 19716 051 Townsend Hall schmi...@udel.edu mailto:schmi...@udel.edu 302-831-1334 ___ 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] Names for genes in RNA-Seq analysis
Regarding the GTF files for cuffllinks, how do I obtain one for all human mRNA that actualy contains gene names rather than accession numbers. I went to the UCSC table browser but their files contain accession numbers that I dont know how to decode en-masse. ___ 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] permanently delete problem
Richard Mark White wrote: hi, so i went to options--saved history--advanced--deleted datasets. then checked all of them, and then hit permanently delete. but nothign happened. they still show up as deleted, and they are taking up lots of my quota. how do i get rid of these? rich Hi Rich, I'm not sure what's going on here, I'm looking in to it. --nate ___ 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] permanently delete problem
actually, i just waited a bit and now they are deletd. r From: Nate Coraor n...@bx.psu.edu To: Richard Mark White whit...@yahoo.com Cc: GANDRILLON OLIVIER olivier.gandril...@univ-lyon1.fr; galaxy-u...@bx.psu.edu galaxy-u...@bx.psu.edu Sent: Wednesday, October 26, 2011 12:55 PM Subject: Re: permanently delete problem Richard Mark White wrote: hi, so i went to options--saved history--advanced--deleted datasets. then checked all of them, and then hit permanently delete. but nothign happened. they still show up as deleted, and they are taking up lots of my quota. how do i get rid of these? rich Hi Rich, I'm not sure what's going on here, I'm looking in to it. --nate___ 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] sample for video for example 3 in ngs analyses in galaxy
Hi, I am watching the video 'Example 3http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html - mapping paired-end Illumina run and visualizing results at UCSC Browser', and would like to try out the exercise. I don't have paired-end Illumina fastq sample, Could you provide me the sample mentioned in the video or point me to the location where I can get a small human paired-end Illumina fastq sample to try out the exercise in example 3. Thanks, Linda McMahan ___ 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] permanently delete problem
Great, thanks for letting us know. Richard Mark White wrote: actually, i just waited a bit and now they are deletd. r From: Nate Coraor n...@bx.psu.edu To: Richard Mark White whit...@yahoo.com Cc: GANDRILLON OLIVIER olivier.gandril...@univ-lyon1.fr; galaxy-u...@bx.psu.edu galaxy-u...@bx.psu.edu Sent: Wednesday, October 26, 2011 12:55 PM Subject: Re: permanently delete problem Richard Mark White wrote: hi, so i went to options--saved history--advanced--deleted datasets. then checked all of them, and then hit permanently delete. but nothign happened. they still show up as deleted, and they are taking up lots of my quota. how do i get rid of these? rich Hi Rich, I'm not sure what's going on here, I'm looking in to it. --nate ___ 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] Genome database/builds missing?
I've been using galaxy to analyze maf files and today the drop down list for database/builds for genomes has lost most of the genomes once listed. I no longer see any bacteria or plants on the list, specifically TAIR9 arabidopsis is no longer on the drop down list when it was just yesterday. Did something change? Thanks - Dan ___ 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] cluster install
Dear Galaxy - We would like to install and instance of Galaxy on our campus cluster. The install process looks very straight forward, but tying it in with our authentication system for the current, functioning cluster may not be as simple. It appears that galaxy is easy to install if there are limited users on a local machine or on a cluster where galaxy is the main use of the cluster (so it handles all the user accounts). Where would I direct our IT admin group to get more assistance with customizing the authentication process with our existing, function cluster? -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA ___ 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] cluster install
Dear Galaxy - We would like to install and instance of Galaxy on our campus cluster. The install process looks very straight forward, but tying it in with our authentication system for the current, functioning cluster may not be as simple. It appears that galaxy is easy to install if there are limited users on a local machine or on a cluster where galaxy is the main use of the cluster (so it handles all the user accounts). Where would I direct our IT admin group to get more assistance with customizing the authentication process with our existing, function cluster? -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307tel:801-422-9307 Fax: 801-422-0008tel:801-422-0008 USA ___ 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] cluster install
It's reasonably easy to set up Galaxy to use external authentication. We modeled our authentication after the way MSI folks did it as posted on the galaxy-dev list a while ago. We use SSO (Single Sign On) with mod_auth_tkt SSO tied into an LDAP back-end used for our cluster. I'd be happy to share the details beyond the LDAP authentication discussion you can find in the Galaxy list archives [1] if necessary. In addition, this sort of question is more appropriate to the galaxy-dev, but not the galaxy-user list. Regards, Alex -- Oleksandr Moskalenko, Ph.D. Biological Applications Support High Performance Computing Center University of Florida 1. http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002660.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002667.html On Oct 26, 2011, at 12:29 PM, Joshua Udall wrote: Dear Galaxy - We would like to install and instance of Galaxy on our campus cluster. The install process looks very straight forward, but tying it in with our authentication system for the current, functioning cluster may not be as simple. It appears that galaxy is easy to install if there are limited users on a local machine or on a cluster where galaxy is the main use of the cluster (so it handles all the user accounts). Where would I direct our IT admin group to get more assistance with customizing the authentication process with our existing, function cluster? -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA ___ 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/
[galaxy-user] Problem with bam and/or bai files
Hello Galaxy Team, I have been using Galaxy for SNP detection for with great success. Basically, I followed the screen-cast from Anton without any problems. The only change was to use the BWA instead of Bowtie. Until now, I have always assigned my raw read files to the hg19 format. Now I want to try the GATK pipeline to analyze my samples but I am running into a problem with the bam/bai files. Here is what I did. I imported my Illumina paired end reads into Galaxy and assigned them to the hg_g1k_v37 format instead of the Hg19 format. From there, I again followed the exact same process: FastQ Groomer, Summary Statistics, Boxplots, Align with BWA, filter on SAM, SAM-to-Bam, generate bai file. I made sure that hg_g1k_37 was chosen for the format for all of these steps that required that information. Everything seemed to run successfully as all of the boxed turned green. When I tried to view the bam file in IGV (as a QC step before the GATK pipeline), I received the following error: Error reading bam file. This usually indicates a problem with the index (bai) file. ArrayIndexOutofBoundsException: 4682 (4682). I did the exact same analysis using the Hg19 format and my bam/bai files worked perfectly fine in the IGV viewer. Can anyone tell me what the problem is and how to fix it? Thanks, Mike Dufault ___ 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] Problem with bam and/or bai files
Hi Mike, Someone from the Galaxy team can perhaps give some insight on what went wrong, I can comment on the error message from IGV. That error is thrown from Picard, in every case I've investigated so far it was traced to a problem with the index. The most common causes are (1) a problem with the sequence dictionary in the BAM header itself, specifically incorrect sequence lengths, and (2) indexing an un-sorted BAM. Apparently samtools will make invalid indexes from such files without any complaints in both cases. You can even use samtools tview on such files, it happily will show you some random region when you query. I don't see a Sort step in your workflow, maybe that's the problem? Please CC me on any reply, I might miss it in the list. Jim Hello Galaxy Team, I have been using Galaxy for SNP detection for with great success. Basically, I followed the screen-cast from Anton without any problems. The only change was to use the BWA instead of Bowtie. Until now, I have always assigned my raw read files to the hg19 format. Now I want to try the GATK pipeline to analyze my samples but I am running into a problem with the bam/bai files. Here is what I did. I imported my Illumina paired end reads into Galaxy and assigned them to the hg_g1k_v37 format instead of the Hg19 format. From there, I again followed the exact same process: FastQ Groomer, Summary Statistics, Boxplots, Align with BWA, filter on SAM, SAM-to-Bam, generate bai file. I made sure that hg_g1k_37 was chosen for the format for all of these steps that required that information. Everything seemed to run successfully as all of the boxed turned green. When I tried to view the bam file in IGV (as a QC step before the GATK pipeline), I received the following error: Error reading bam file. This usually indicates a problem with the index (bai) file. ArrayIndexOutofBoundsException: 4682 (4682). I did the exact same analysis using the Hg19 format and my bam/bai files worked perfectly fine in the IGV viewer. Can anyone tell me what the problem is and how to fix it? Thanks, Mike Dufault ___ 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/
