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

Walltime exceeded
by Hemarajata, Peera 30 Jan '12

30 Jan '12

Dear all, My Cufflinks jobs keep getting killed due to the walltime limit. Is there a way to fix this or is there anything I can do to reduce the size of my BAM datasets so the analysis can get done? Thank you! Peera Hemarajata

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BioCloud Cenral - More Instance types options?
by mailing list 30 Jan '12

30 Jan '12

What do you guys think about having more instance type options on the BioCloud Central launch page? I am interested in using the "Hi-Memory On-Demand Instances". Would CloudMan/Galaxy have any problems running on those instances? Thanks, Greg

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January 27, 2012 Galaxy Distribution & News Brief
by Jennifer Jackson 27 Jan '12

27 Jan '12

January 27, 2012 Galaxy Distribution & News Brief Complete News Brief * http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_27 Highlights: * Important metadata and Python 2.5 support corrections * SAMtools upgraded for version 0.1.18. Mpileup added. * Dynamic filtering, easy color options, and quicker indexing enhance Trackster * Set up your Galaxy instance to run cluster jobs as the real user, not the Galaxy owner * Improvements to metadata handling and searching in the Tool Shed * Improved solutions for schema access, jobs management, & workflow imports and inputs. * New datatypes (Eland, XML), multiple tool enhancements, and bug fixes. Get Galaxy! * http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 26920e20157f Read the release announcement and see the prior release history * http://wiki.g2.bx.psu.edu/DevNewsBriefs/ Need help with a local instance? Search with our custom google tools! * http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching And consider subscribing to the galaxy-dev mailing list! * http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing -- Jennifer Jackson Galaxy Team http://usegalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki/Support

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New Genome Load Request
by Mark Guiltinan 26 Jan '12

26 Jan '12

Hello Galaxy, Would you please perform the following new genome load? Theobroma cacao All the necessary resource files can be found and downloaded at: http://cocoagendb.cirad.fr/gbrowse/download.html Thank you Mark Guiltinan Mark Guiltinan Professor of Plant Molecular Biology Penn State University Department of Horticulture 422 Life Sciences Building University Park, PA 16802-5807 Phone 814 863-7957 mjg9(a)psu.edu Web Site: http://guiltinanlab.cas.psu.edu

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Removing duplicate lines from a table
by Sébastien Vigneau 26 Jan '12

26 Jan '12

Hi, I have a table and would like to remove duplicate lines based on values in the first column. Is there a simple way to do it in Galaxy? Thanks, Sebastien

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Cufflinks merging more than one transcript on bacterial genomes
by Noa Sher 25 Jan '12

25 Jan '12

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BioCloudCentral - First Launch Not Working
by mailing list 25 Jan '12

25 Jan '12

Hi guys, For the past two days when I try to launch my CloudMan instance using http://biocloudcentral.herokuapp.com the first time I see an instance get up and running, but it doesn't mount my galaxyData volume and I can't get to the webpage <public DNS>/cloud. The webpage just says "Unable to connect. Firefox can't establish a connection to the server at ...". If I terminate the instance and relaunch through BioCloudCentral it seems to then start up fine. Any ideas? Is there any more information I can provide to help? Thanks, Greg

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Cloudman - Cluster could not complete job errors
by Dave Lin 25 Jan '12

25 Jan '12

Dear Galaxy Team, I seem to get quite a few "Cluster could not complete job" error messages when trying to process larger solid files. In some cases, re-running the same job does the trick. Is this due to something I've misconfigured (i.e. some time-out setting) or is this expected behavior? Any suggestions (i.e. increase number of nodes)? Details - Running own instance of Galaxy using Cloudman - Galaxy code is updated (within 1 week) - Only have 1 node running. - Nobody else is using the system yet. Thanks, Dave P.S. New to galaxy and pretty impressed so far. Running the Galaxy

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CloudMan - SGE / Cluster Questions
by mailing list 24 Jan '12

24 Jan '12

Hi guys, So I'm trying to take a bioinformatics pipeline we currently run on our own SGE cluster (which seems to have a lot of customizations ! I'm finding out) and I want to run it on Amazon using CloudMan. So I'm trying to figure out what the differences are. Here are my questions so far: We seem to have 8 slots per node. Do you guys know if the same is true on CloudMan? I'm assuming more than one submitted qsub job can run on one node at one time? Also is there a way to reserve a certain amount of memory for a job submitted via qsub, or alternatively to request that the job have exclusive access to a node so it keeps all the memory available? Thanks, Greg

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Resuming FTP uploads to main server
by Hemarajata, Peera 24 Jan '12

24 Jan '12

Dear all, I have not been able to resume any of my interrupted uploads via FTP to the main Galaxy server. I use FileZilla and every time I click the "resume" button, instead of resuming from where it left off, the transfer always starts from scratch. Would anybody be able to tell me what I might be doing wrong? Thank you! 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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