- galaxy-user - lists.galaxyproject.org

FASTQ joiner
by lilach noy 11 Sep '13

11 Sep '13

Hi all, Has anyone used FASTQ joiner with a file containing multi-mapped reads? I'm pretty sure i have reads mapped to several locations and i don't know what this tool does with it? will it locate the right map according to the paired read? will it use the first read location and ignore the rest or maybe it will exclude all multi-mapped reads prior to paring? Regards, Lilach

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error message from Filezilla
by Amit Pande 11 Sep '13

11 Sep '13

Hi, I am getting the following error from the server : Command: USER genebuster(a)googlemail.com Response: 331 Password required for genebuster(a)googlemail.com Command: PASS *********** Response: 530 Sorry, the maximum number of clients (3) for this user are already connected. Error: Critical error Error: Could not connect to server. Can you please help. warm regards, Amit.

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cannot download data to Galaxy
by Elwood Linney 11 Sep '13

11 Sep '13

Hello, My connection with Galaxy online shutoff last night while I was transferring data to it. When I tried to connect again with Fetch this morning I was not allowed and a message like "Sorry the maximum number of clients for this user are already connected." I have had what appears to be the bad habit of not logging off to Galaxy. I am working on the same data sets with three different computers, I only have one login to Galaxy, so yes, I was logged in on 3 different computers. When I logged off of them, and tried to transfer data, I still got the same message. I realize people might be trying to get around the 250gb limit by having multiple logins--I am not one of them, I am the only user on the three computers I am using. If not logging off when I leave the computer is a problem to Galaxy, I will religiously log off each time I am not using the computer (the computers are in three different rooms in my lab and my lab consists of just me and a tech--I am the only one who knows the computer login for both the computers and for Galaxy). If I have created a problem by being "lazy", I apologize, but I have grown dependent upon using Galaxy online and some new data just came in. Sincerely, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Center

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GATK error Argument with name 'T' isn't defined
by Erica Westerman 11 Sep '13

11 Sep '13

Aloha. I am using GATK in Galaxy for the first time, on a local Galaxy server, and when I try to run Count Covariates I get the error: ERROR stack trace org.broadinstitute.sting.commandline.InvalidArgumentException: Argument with name 'T' isn't defined. at org.broadinstitute.s I have looked at the GATK Count Covariates command line, and it looks to me like the argument with name 'T' is not a place where I need to input a file, but is where the Count Covariates software information goes. I get this same error when trying to run Realigner Target Creator. I wondered if this might be something that could be simply fixed by reinstalling the wrappers for GATK, or something along those lines? Thank you!

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Galaxy main server down?
by Boaz Shaanan 09 Sep '13

09 Sep '13

Hi, Any idea when the server is going to be up again? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Joachim Jacob | VIB | [joachim.jacob(a)vib.be] Sent: Friday, September 06, 2013 10:32 AM To: kanwarjag(a)gmail.com Cc: galaxy-user(a)bx.psu.edu Subject: Re: [galaxy-user] Bam QC and coverage Hi Shamsher, Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at: http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite You need to install this tool in a local Galaxy, with the qualimap suite installed and perl (see README). Cheers, Joachim > On 09/04/2013 09:59 PM, shamsher jagat wrote: > I am looking for a tool to perform QC of Bam file especially following > functions: > 1. BAsic information and stat. > 2. Coverage across reference features- gene/ transcripts. > Is it possible to do it in Galaxy? > Thanks -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___________________________________________________________ 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/

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Zooming in and out in Circster
by Ian Donaldson 09 Sep '13

09 Sep '13

Sorry if I am missing some instructions somewhere, but how do you zoom out of a Circster plot? I have zoomed in by double clicking, but cannot work out how to zoom back out? Thanks, Ian

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Re: [galaxy-user] Bam QC and coverage
by Joachim Jacob | VIB | 06 Sep '13

06 Sep '13

Hi Shamsher, Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at: http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite You need to install this tool in a local Galaxy, with the qualimap suite installed and perl (see README). Cheers, Joachim > On 09/04/2013 09:59 PM, shamsher jagat wrote: > I am looking for a tool to perform QC of Bam file especially following > functions: > 1. BAsic information and stat. > 2. Coverage across reference features- gene/ transcripts. > Is it possible to do it in Galaxy? > Thanks -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Re: [galaxy-user] For constructing workflow of workflows
by Jennifer Jackson 06 Sep '13

06 Sep '13

Hi Deblina, The way to track progress is to watch the Trello card. It is always difficult to give reliable estimates with projects still in progress, but I can let you know that this is an important development area for us and it has priority. Take care, Jen Galaxy team On 9/5/13 2:46 PM, patra wrote: > Hi Jen, > > Thanks a lot for your reply and letting me know that the > concept is in progress as of now. Can you please let me know how much > time approximately it can take to implement the concept of the "nested > workflows" into galaxy? > > Best Regards, > Deblina. -- Jennifer Hillman-Jackson http://galaxyproject.org

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version_command tag problem
by Wolfgang Maier 05 Sep '13

05 Sep '13

Hi everybody, I'm trying to add the version_command tag to my tools' xml files, but I run into a problem here. Currently I have: <version_command interpreter="python3">aln.py --version</version_command> in my xml. When I run the tool Galaxy tells me that it executed this: python3 /home/me/galaxy-dist/tools/modmapmin/aln.py --version &> /home/me/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1035 but when I check that temporary file it's empty (and so is the tool version line at the end of the run). This is puzzling because when I run that exact command line from my terminal, it writes 0.8.2 to the file just as it should. Any ideas what goes wrong here? Thanks and best wishes, Wolfgang

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NoClassDefFoundError in Picard Paired Read Mate Fixer
by Nicolas Quizon 05 Sep '13

05 Sep '13

Dear Galaxy Gurus, I am a student and still new to Galaxy. I am encountering an error when trying to run the Picard Paired Read Mate Fixer with default settings on Galaxy. The code only runs for a few seconds before failing and displaying the error message. ## exit code=1; stdout= [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation INPUT=[/usr/lib/galaxy-server/database/files/000/dataset_85.dat] OUTPUT=/usr/lib/galaxy-server/database/tmp/tmpxhbz3T SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Aug 19 16:46:15 EDT 2013] Executing as root@biolinux-pbcn6 on Linux 3.2.0-43-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_27-b27; Picard version: 1.91() [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=378470400 To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp Exception in thread "main" java.lang.NoClassDefFoundError: org/itadaki/bzip2/BZip2InputStream at net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:84) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:76) Caused by: java.lang.ClassNotFoundException: org.itadaki.bzip2.BZip2InputStream at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) ... 4 more For input I am using data that I have successfully mapped with BWA for Illumina. I currently have Python version 2.7.3 and Java version 1.6.0_27, and an working on a machine running Ubuntu 12.04.2 LTS. Any help is greatly appreciated! Thanks!

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