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

Advice on disabling SGE queue on galaxy-cloudman
by John Major 07 Mar '12

07 Mar '12

Hello All- I'd like to launch a galaxy-cloudman head node which does not accept SGE jobs, but as jobs are submitted go to compute nodes (or cause compute node to be added when auto-scale is on). Primarily, this is b/c I'd like to have the head node be a cheaper instance which can run long term, and only fire up more expensive compute nodes as they are actually needed. How would I enable this? Thanks- John

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Cufflink not working
by Ateequr Rehman 06 Mar '12

06 Mar '12

Dear Galxy admin and user I have generated BAM file from my RNa seq data by using Bowtie with custom reference, followed by Filter SAM and SAM to BAM connversion, i wish to run cufflink, but its just givinbg me emty file, any suggestion, how to proceed Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau

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Problem using Galaxy on the cloud
by Jan R McDowell 06 Mar '12

06 Mar '12

Hi all, I have been trying to get an instance of Galaxy going on the EC2. I have no problem going through BioCloudCentral and getting an instance going. I can also successfully load my data from an S2 bucket into Galaxy. The problem occurs when I try to use velveth. I always says 'job waiting to run'. As a matter of curiosity, I then used SSH to get into CloudBioLinux, which worked. However, when I try to use NX to get the virtual desktop going I get the message usr/bin/nxserver: line 381: echo: write error: No space left on device. Using the df -h command, I get: Filesystem Size Used Avail Use% Mounted on /dev/xvda1 20G 19G 0 100% / udev 8.4G 4.0K 8.4G 1% /dev tmpfs 3.4G 660K 3.4G 1% /run none 5.0M 0 5.0M 0% /run/lock none 8.4G 0 8.4G 0% /run/shm /dev/xvdb 404G 202M 383G 1% /mnt /dev/xvdg1 700G 654G 47G 94% /mnt/galaxyIndices /dev/xvdg2 10G 1.7G 8.4G 17% /mnt/galaxyTools /dev/xvdg3 200G 11G 190G 6% /mnt/galaxyData So, I guess my question as a new user is: How do I point Galaxy and CloudBioLinux to all of this unused space? I assume the problem is with the /dev/xvda1 that is 100% full. I am obviously doing something silly and/or missing a really big step. Any help would be greatly appreciated. Many thanks in advance, Jan

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Variable number of inputs in Workflow (or optional inputs)
by Daniel Sobral 06 Mar '12

06 Mar '12

Hi, I wanted to build a workflow where the first step would be a tool that can have a variable number of inputs (e.g. a series). It seems that I need to predefine apriori the number of inputs to give to the tool. Is there a way to define the number of inputs at runtime? E.g. a series-like input? Thanks, Daniel

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BAM to SAM
by Matthew McCormack 06 Mar '12

06 Mar '12

SAM-to-BAM (version 1.1.2) says that it produces an indexed BAM file based on a sorted input SAM file. When I go from SAM to BAM using SAMTools on my computer (not using Galaxy), I first convert the SAM to BAM then sort the BAM. I was wondering if on Galaxy you need to first sort the SAM file then use SAM-to-BAM to get the same result ? Matthew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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April GMOD meeting early registration
by Scott Cain 06 Mar '12

06 Mar '12

Hello, This is a reminder that there is only a little over two days left to get in on early registration for the April 2012 GMOD meeting. In addition to getting a $10 discount on the registration fee, you will be entered in a drawing to get a GMOD coffee cup or T-shirt. There are some very good speakers and topics lined up for the meeting; I'm looking forward to a good one. Please see: http://gmod.org/wiki/April_2012_GMOD_Meeting for more information on the meeting, and to: http://gmod2012.eventbrite.com/ to register for the meeting. I look forward to seeing you next month. Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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Galaxy unable to set metadata for GFF files
by Hemarajata, Peera 05 Mar '12

05 Mar '12

Dear all, I'm been trying to get Galaxy to recognize this GFF from NCBI ( ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Lactobacillus_reuteri_JCM_1112_uid5…) but it failed to recognize the format after I uploaded it. Manual setting didn't work either because it gave me a "unable to set metadata" error to me as soon as I started a cufflinks run using that GFF. I have tried to reformat the file several times and even tried using the popular bp_genbank2gff3.pl script to re-parse the records from the original genbank file. Would anyone kindly look at the NCBI GFF and guide me to a solution to get this file recognized by Galaxy? I've been stuck for a couple of weeks now and would appreciate some suggestions. Thank you! Sincerely yours, Peera Hemarajata, M.D. Advanced graduate student - Versalovic lab Department of Molecular Virology and Microbiology - Baylor College of Medicine Department of Pathology - Texas Children's Hospital Suite 830, 8th Floor Feigin Center. Tel: 832-824-8245

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Production environment and Apache's sendfile
by Yuri D'Elia 05 Mar '12

05 Mar '12

Hi everyone. I've set up a galaxy production environment and it seems to be working. I've identified a couple of issues though: If I enable apache_xsendfile, the little "eye" icon ("Display data in browser") on each dataset stops working. I get the following instead: The requested URL /datasets/7e93e3cf926fb2b3/display/ was not found on this server My document root is not the same as the galaxy root (as suggested). Everything else seems to work. Is this a bug? Second question: I want to rotate the galaxy log file (as specified with paster.py serve --log-file. I can't find a way to reopen the logfile in galaxy without taking down the whole service, or a way to redirect the log to a pipe together while using --daemon. I cannot let the file grow forever. Any suggestions? Thanks.

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Progress indicators/feedback for long jobs on Galaxy
by Greg Edwards 05 Mar '12

05 Mar '12

Hi, This has been raised a number of times .. one issue is at ... https://bitbucket.org/galaxy/galaxy-central/issue/250/progress-of-running-j… but seems to have been dropped from Open to On Hold. There was another similar request in the issues list but I can't find it just now. I'd be gald to know if anything is happening on the idea of simple progress indicators. The first things that were raised by my "users" were 1) Don't know how long a data upload is going to take, and b) Don't know what's happening with my tool execution. (And these were both operations of only 5-10 minutes or so, they'd go crazy with the multi-GB uploads and hours-long runs I see reported here). I've implemented my own email-based scheme on a AWS EC2 CloudMan Galay, seems to be working ok. It uses an Ubuntu package "sendEmail", which is a self-conatined simple SMTP email sender. It sends progress emails out of the main Perl tool code, via a bash script, every 1 to N minutes (selectable), to an email address supplied by the user. The emails have configurable subject and content with brief display of Start, Progress (every N minutes) and Success/Failure termination status. You have to jump through some hurdles. AWS thinks your'e a spammer and blocks emails after a while ! but you can submit a request to get around that. If anyone's interested let me know. Cheers, Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwards2(a)gmail.com

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Error on custom builds on public galaxy server
by David Beck 02 Mar '12

02 Mar '12

I am having a problem with the public galaxy server. When I try to go the User->Custom Builds page, I see the following error: -- Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) -- I had previously created a custom build but when I try to use it, for example in a BWA/Illumina alignment, I get the following error: -- Error executing tool: maximum recursion depth exceeded while calling a Python object -- I believe this is a continuation of a previous thread that was started before I joined the list: http://galaxy-users-list-archive.2308625.n4.nabble.com/Error-on-custom-buil… Thanks for any help. -- David A. C. Beck, Ph.D. eScience Institute University of Washington, Seattle

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