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

July 2012 Galaxy Update
by Dave Clements 29 Jun '12

29 Jun '12

Hello all, The July 2012 Galaxy Update is now available<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07>. *Highlights:* - GCC2012 is July 25-27!<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#GCC2012_is_July_25-27.21> - Register by July 18<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> - Other Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Upcoming_Events_and_Deadlin…> ,* including these deadlines in the next several days* - Galaxy Workshops in South Africa<http://wiki.g2.bx.psu.edu/News/GalaxyWorkshopsInSouthAfrica>(deadline: *June 30*) and the South African Genetics & Bioinformatics Society Conference <http://genetics.cmc-uct.co.za/> (deadline *July 1*) - Systems Bioinformatics Workshop<http://gaggle.systemsbiology.net/workshop2012/>(deadline: *June 30*) - GMOD Summer School<http://gmod.org/wiki/2012%20GMOD%20Summer%20School>(deadline: *July 9*) - 31 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Papers>, including two new *Current Protocols* - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Who.27s_Hiring>at six different institutions - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Tool_Shed_Contributions> - A new CloudMan distribution was released last month<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Distributions> - Plus <http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Other_News> - Easily wrap your R functions as Galaxy tools - help schedule the first GalaxyCzars<http://wiki.g2.bx.psu.edu/Community/GalaxyCzars>conference call on July 9 or 10 - and lots of new screencasts, tutorials, and new genomes on main If you have anything you would like to see in the August *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave Clements -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Re: [galaxy-user] Data upload issues on Galaxy
by Fatih Ozsolak 28 Jun '12

28 Jun '12

Hi Jennifer, I had some uploads that were probably stuck and going on for 5-7 days. I deleted them and uploaded 2 new files for upload. can you please check and see if the upload is happening normally for these files? Thanks a lot for your help and patience thanks, fatih On Wed, Jun 20, 2012 at 10:43 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hello Fatih, > > I found five jobs under your account in the NGS cluster queue. Job > processing is normal - the Galaxy main instance is just very busy today. > Your jobs will process in the order that they were queued (the size of the > jobs does not impact how long it takes for them to begin to run, only when > they where started with respect to other jobs and how long those earlier > jobs take to complete). There are substantial resources dedicated to the > public instance, so I would expect your jobs to begin to process within the > next 24 hrs (at the latest). > > If your work is urgent, a cloud instance is the recommended alternative: > http://getgalaxy.org/cloud > > Best, > > Jen > Galaxy team > > > On 6/20/12 6:44 PM, Fatih Ozsolak wrote: > > Hi, > > I submitted Bowtie and BWA alignment jobs on two relatively small fastq > files, and the jobs still appear as gray after multiple hours. can you > please check and see if the system if functioning properly? > > thanks, > fatih > > > ___________________________________________________________ > 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 Jacksonhttp://galaxyproject.org > > > >

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Problem with Depth of Coverage on BAM files (GATK tools)
by Lilach Friedman 28 Jun '12

28 Jun '12

Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals. I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) and the intervals file (in advanced GATK options). The consensus genome is hg_g1k_v37. I got the following error message: An error occurred running this job: *Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): ##### ERROR The invalid argume *Is it a bug, or did I do anything wrong? I will be grateful for any help. Thanks! Lilach* *

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Cannot upload file to data library
by Ciara Ledero 27 Jun '12

27 Jun '12

Hi all, I created an account in our local Galaxy instance and it's a non-admin one. I have set up Galaxy (I have an account that's an admin) so that my user account can upload files to a data library. But when I tried doing it, I got the following error: The directory <some folder here> contains no valid files. I checked the path to the folder and it was correct. I also checked if I had really placed the FASTQ file inside the folder and I found the file there. Why is Galaxy telling me that there is no valid file within the folder when there's a file present within the directory? Thank you in advance for any help! CL

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Re: [galaxy-user] Quick question about cuff compare
by Jennifer Jackson 27 Jun '12

27 Jun '12

Hello Jason, The short answer is that the database is interpreted from the database assignment of the inputs to the tool. Have you seen our RNA-seq tutorial? It may answer some of the other questions. http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Best, Jen Galaxy team On 6/26/12 2:02 PM, Jason Serviss wrote: > Hello Jennifer, > > Thank you for your prompt reply! Yes, I am using the public main > Galaxy at the link you included. So just to clarify (sorry its my > first time doing this), if I select "locally cached" the analysis will > automatically be done with a Sequence Data file located on the server? > How is the proper species Sequence Data selected (i.e. h19 in this > case) and the version? I didn't receive a prompt to select any > specific database after clicking the "locally cached" option. Do I > need to place h19 in my history? I looked in Galaxy for a link to > "Cuff*RNA-seq tools (which you had mentioned), but couldn't manage to > locate it... Thanks for your patience! > > Kind Regards, > Jason > > 2012/6/26, Jennifer Jackson <jen(a)bx.psu.edu>: >> Hello Jason, >> >> Are you using the public main Galaxy instance at >> http://main.g2.bx.psu.edu (usegalaxy.org)? The hg19 database can be used >> as a "locally cached" reference genome with the Cuff* RNA-seq tools, so >> there isn't any need to load external fasta files. If you do decide to >> use a custom genome in the future (a different genome), individual >> chromosomes can be merged with the tool "Text Manipulation -> >> Concatenate datasets". >> >> More help with format is on our wiki: >> http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome >> >> Thanks, >> >> Jen >> Galaxy team >> >> On 6/26/12 8:50 AM, Jason Serviss wrote: >>> Hi! >>> >>> Just a quick question.... I am trying to use cuffcompare for human >>> data and want to use a Sequence Data (h19). I can only seem to find >>> the fasta files divided by chromosome. If I upload all of these files >>> individually will the program be able to simultaneously use the files >>> (it looks as though there is only space to input 1 file...)? Or do I >>> need to find the whole genome in 1 Sequence Data file? Thanks in >>> advance for your help! >>> >>> >>> Kind Regards, >>> Jason >>> ___________________________________________________________ >>> 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 >> >> >> >> -- Jennifer Jackson http://galaxyproject.org

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[galaxy-user] Complete Genomics CGA Tools™� in Galaxy
by Birgit Crain 27 Jun '12

27 Jun '12

Dear Community Members Complete Genomics, Inc<http://www.completegenomics.com/>. is happy to announce the release of a CGA Tools™ implementation in Galaxy. CGA Tools™ is an open source project<http://cgatools.sourceforge.net/> to provide tools for downstream analysis of Complete Genomics Whole Genome Sequencing data. This first release includes the most commonly used functions of CGA Tools™ such as listvariants, testvariants, calldiff, snpdiff, junctiondiff, join and varfilter. Ongoing development will add other functions of CGA Tools™, which were not part of this release, and a variety of data analysis workflows. There are two repositories available for download from the Galaxy Tools Shed<http://toolshed.g2.bx.psu.edu/>: a linux version, cg_cgatools_linux, and a Mac OSX version, cg_cgatools_mac_osx. Both repositories are bundled with the latest version of CGA Tools™ (1.5.0.31) for the respective operating system and contain instructions for automated and manual installation of the tools, as well as instructions for the download and installation of reference genome files. Please reply to this post with any comments to this release and suggestions for future development, or contact us at ProfServ(a)completegenomics.com<mailto:ProfServ@completegenomics.com> Best regards Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. ________________________________ The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation.

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Quick question about cuff compare
by Jason Serviss 27 Jun '12

27 Jun '12

Hi! Just a quick question.... I am trying to use cuffcompare for human data and want to use a Sequence Data (h19). I can only seem to find the fasta files divided by chromosome. If I upload all of these files individually will the program be able to simultaneously use the files (it looks as though there is only space to input 1 file...)? Or do I need to find the whole genome in 1 Sequence Data file? Thanks in advance for your help! Kind Regards, Jason

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How to revive my account that had been marked as "deleted"?
by 碩璜陳 26 Jun '12

26 Jun '12

Dear all, Has any one encounter this situation that the public galaxy server sent back this message as I tried to log in my account, "This account has been marked deleted, contact your Galaxy administrator to restore the account." How can I deal with this problem? I thought it was possible that I had run more than 8 jobs concurrently, so the server automatically deleted my account. How do I revive my account, and any one know what is the galaxy administrator's email? I thanks a lot in advance. Pathomida

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Converting to index files of viral genome for running TopHAT
by shamsher jagat 26 Jun '12

26 Jun '12

I was wondering if it is some how possible in galaxy to format FAST genome seq file of microbial genome to format to generate bowtie index so that it can be used for RNA seq analysis using TopHat. Alternatively any pointer to an available tool which can generate index files. Thanks Kanwar

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Job is waiting to run for two days..
by Shanshan Pang 26 Jun '12

26 Jun '12

Hi, I am in the step "map with bowtie" with a status of JOB IS WAITING TO RUN for two days. I tried to re-run it, but did not work. So any suggestions on it? Thanks! Shanshan

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