galaxy-dev December 2011

galaxy-dev@lists.galaxyproject.org

85 participants
126 discussions

Display VCF in IGV problem
by Lance Parsons 05 Dec '11

05 Dec '11

I am unable to get VCF files to display in IGV in my local galaxy installation. BAM files display fine, however, whenever I click on the link to display a VCF file I get the following error message: "You must import this dataset into your current history before you can view it at the desired display application." When I return to Galaxy, my history is indeed changed to a new empty history. I think this may have to do with the fact that I had to setup Apache to allow unauthenticated access to the bam/vcf files (see my notes on how I did this at https://sites.google.com/site/princetonhtseq/tutorials/visualization-with-g…). However, I can't figure out why BAM files work and VCF files don't. Any advice or insight would be appreciated. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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GATK / R local install configuration
by Carlos Borroto 05 Dec '11

05 Dec '11

Hi, I'm testing the GATK pipeline and I ran into a problem with "Variant Recalibrator" tool. It seems I don't have correctly configure R and GATK on my instance, as this tool is failing with this error: mv: /Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat.pdf: No such file or directory I see this PDF is builded with R and I also see this in the log file: INFO 17:11:44,260 VariantRecalibrator - Executing: Rscript /Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat WARN 17:11:48,407 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. In the testing server this tool does work: http://test.g2.bx.psu.edu/u/cjav/h/variant-recalibrator---tutorial At least after making sure the input VCF file has matching annotations string to the one you want to select in Galaxy. Any help on what need to be done to get this configuration right. BTW I already have R and Rpy correctly configured and I can run tools like "Statistics/Summary Statistics". Thanks! Carlos

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Re: [galaxy-dev] [galaxy-user] Upload executable in galaxy
by Nate Coraor 05 Dec '11

05 Dec '11

On Nov 23, 2011, at 11:10 AM, Giota Kottara wrote: > Dear galaxy developers, > > I am trying to integrate an executable tool in a private instance of galaxy. I stored the configuration .xml file and the executable in tools folder of Galaxy and the tool appears in the homepage. Nevertheless when i am running the tool it doesn't seem to find the executable. Am I forgetting something? Hi Giota, I've moved this over to the galaxy-dev list since it pertains to tool development. Executables will need to be on the $PATH of the user running Galaxy. Could you share the error messages you receive when you run the tool? --nate > > Thank you in advance > Giota Kottara > ___________________________________________________________ > 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/

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Urgent help needed
by Toqa Manasrah 05 Dec '11

05 Dec '11

Hi Everybody, I am running a tool which is not defining the output file name as parameter. the tool is running and I can see the output file in the history directory but not in the history frame. how could I solve the problem? I should see and download the output file from the history but I see an error message instead. the error message not a real error but rather galaxy cannot figure out which file to display? your help is appreciated, ________________________________________ From: Jennifer Jackson [jen(a)bx.psu.edu] Sent: Tuesday, November 08, 2011 8:22 AM To: Toqa Manasrah Cc: Galaxy Dev Subject: Re: [galaxy-dev] Installing Galaxy on local server Hello Tuqa, Galaxy will not stop by itself. That said, you will want to monitor the instance and any associated cluster, just as you would any other important processes. Please send all follow-up with a cc to the mailing list ("reply-all"). The development community is a great resource for administrative advice and they may have more to add to this reply, i.e. how stable they have found Galaxy to be under various conditions. Best, Jen Galaxy team On 11/8/11 4:01 AM, Toqa Manasrah wrote: > Thank you so much, > > I did the installation and I ran it under my server. > I have one thing concerning about now. if u can help plz. > > how to run Galaxy in such way that the html interface will continuously working and available for all users visiting the page? > > i mean how to guarantee that the "sh run.sh" will keep running without any interrupt? > > Thank you, > Tuqa > > ________________________________________ > From: Jennifer Jackson [jen(a)bx.psu.edu] > Sent: Thursday, November 03, 2011 6:47 PM > To: Toqa Manasrah > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Installing Galaxy on local server > > Hello Toqa, > > From your description, this sounds like a local installation for the > Galaxy instance itself. Then you can add on a cluster (local or cloud) > as needed. > > Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/ > Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed > > Hopefully the documentation is helpful, > > Best, > > Jen > Galaxy team > > On 11/3/11 9:40 AM, Toqa Manasrah wrote: >> Hello, >> >> I am a graduate student at GSU. I am looking for installing GALAXY on >> our local server http://alla.cs.gsu.edu/~software. as a result I like my >> server homepage start with the GALAXY interface, like this one: >> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some >> software tolls that we developed in ourdepartment. my primary question >> is which option Ihave to choose: Local or cloud? >> >> looking forward for your help and directions. >> >> Thank you. >> >> Tuqa >> >> >> >> ___________________________________________________________ >> 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/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Configure Tools/Blast
by Zachary Charlop-Powers 05 Dec '11

05 Dec '11

Hi Galaxy-Dev, I'm a galaxy newbie setting up a local Galaxy server and I am looking for some help on how to customize our local BLAST databases. Right now I can Blast files against one another but I don't know how to let Galaxy know about the databases (nt/nt/refseq/custom, etc) on our server. While the documentation has been pretty great I don't see how to modify BLAST and would appreciate being pointed in the right direction. thanks, zachcp

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Removing nodes from a CloudMan instance
by Clare Sloggett 05 Dec '11

05 Dec '11

Hi galaxy-devs, Quick question: when using the cloud console on CloudMan, it's possible to add different types of nodes (large, micro, etc) to the virtual cluster using the 'Add Nodes' option at the top. I can also remove a given number of nodes using the 'Remove Nodes' option at the top. However, is there any way to control exactly which node (or more importantly just which type of node) gets removed? Thanks for any help! Clare -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759

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PATH env variable for SGE jobs
by Langhorst, Brad 04 Dec '11

04 Dec '11

I have the software for our SGE cluster (eg. Bowtie) in /mnt/ngswork/galaxy/sw/bin And I've set the PATH environment in the galaxy user's .bashrc export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH" When I echo $PATH via qsub as galaxy I do see my path in STDIN.o on the job runner node /mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/usr/bin But I always see /bin/sh: bowtie: not found As an error message. How can I get the path set correctly? Brad -- Brad Langhorst New England Biolabs langhorst(a)neb.com

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proxy settings?
by Smithies, Russell 04 Dec '11

04 Dec '11

I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question . When I try to "Get Data" from UCSC or any other external site, I get a 407 error from our proxy as I need to authenticate. Is the request going out as the 'galaxy' user or 'apache' or the user that's logged in? I already have http_proxy and ftp_proxy configured in /etc/profile (we're running Centos 6) but I assume there a correct place to configure this for Galaxy? The error message I'm seeing is: An error occurred running this job: The remote data source application may be off line, please try again later. Error: ('http error', 407, 'Proxy Access Denied', <httplib.HTTPMessage instance at 0x35d2998>) Any ideas? Thanx, Russell Smithies ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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Define a path for the command files
by Toqa Manasrah 02 Dec '11

02 Dec '11

Hi everybody, I am integrating a new tool which depends on several other libraries (part of the tool). when galaxy run my tool, it can find main command but not the deepest. where should I define the path of the libraries and command folders I need. by teh way, all these commands and libraries are copied inside the tool directory. Thank you,

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Galaxy-Announce: A new, moderated, low-volume Galaxy Mailing List
by Dave Clements 02 Dec '11

02 Dec '11

Hello all, There is a new mailing list in the Galaxy: Galaxy-Announce. Galaxy-Announce is a *moderated, low-volume *mailing list. Galaxy-Announce complements the existing Galaxy-User (about the public server at UseGalaxy.org) and Galaxy-Dev (deployment and development) mailing lists. However, unlike those relatively high-volume mailing lists, Galaxy-Announce will only have a few messages each month. If you are looking for a Galaxy list that just covers the big stuff, this is your list. To subscribe to the list please add your email address to the list here: http://lists.bx.psu.edu/listinfo/galaxy-announce See http://wiki.g2.bx.psu.edu/Mailing%20Lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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galaxy-dev December 2011