June 2011 - galaxy-user - lists.galaxyproject.org

Using a remote cluster
by James Vincent 12 Jun '11

12 Jun '11

Hello, Is it possible to run Galaxy jobs on a remote cluster? For example, I have a server with a complete working Galaxy setup and I would like to have Galaxy submit jobs to a Teragrid resource or a cluster on campus that I do not own. I could not find (or perhaps understand) how one might run Galaxy jobs on a remote cluster. It seems the detailed instructions for running on a cluster assume you "own" the cluster. Is it still possible if one is a regular user only? Thanks, Jim

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Fastq uploads
by Keith Giles 12 Jun '11

12 Jun '11

I converted 2 fastq datasets, roughly 3 gb in size each. They have been queued up for about 24 hours now. Are they too big? What is the best way to upload large fastq datasets? Sent from my iPhone

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Videos online of the Galaxy community conference 2011
by Marc van Driel 10 Jun '11

10 Jun '11

Hello all, Thanks to all speakers and participants of the Galaxy Community Conference 2011. You made this an excellent meeting. Videos are now available at http://vimeo.com/nbic Feedback: Please give your feedback on the meeting to the Galaxy team. A short, one-page survey is at http://bit.ly/ltUnyj This information will be used when planning future Galaxy events. Best, Marc _____________________________________________________ Marc A. van Driel (PhD) Netherlands Bioinformatics Centre Coordinator Bioinformatics 260 NBIC P.O. Box 9101 6500 HB Nijmegen Tel. +31 (0)24 36 19500 (NBIC Office) Tel. +31 (0)24 36 13306 (Direct) Tel. +31 (0)6 24448612 (Mobile) Skype: marc.van.driel Fax. +31 (0)24 89 01 798 E.mail marc.van.driel(a)nbic.nl<mailto:marc.van.driel@nbic.nl> http://www.nbic.nl _____________________________________________________

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extract alignment for a set of genes
by Vincent Joseph Lynch 10 Jun '11

10 Jun '11

To Whom It May Concern, Sorry to bother you with what is likely a fairly simple problem, but I have trying to figure this out myself for several days and just can't figure out how to do it. I have a set of 8766 genes that I would like to test for positive selection in using various other programs (HyPhy for example). To do this I obviously need an alignment of these genes across various species, but I just can't figure out how to get the alignment in a fasta format. For example, I have a BED12 file from UCSC with the data for the 8766 genes, I thought the easiest way was to use the "Stitch Gene blocks" option and then select locally cached alignments as the MAF source for the species I care about. However, because these 8766 genes have multiple transcripts I end up with 23,581 regions. Is there a way to merge the multiple regions for each gene into a single region for the longest transcript? Then I should have 8766 regions and can use Stitch Gene blocks". (Unless there is a more economical way to do this.)\ Thanks Vinny Vincent J. Lynch, Associate Research Scientist Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute Yale University http://pantheon.yale.edu/~vjl4/profpage/ "There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." -C. Darwin, 1859 (Walker, Wisconsin, Madison, Maddow, Tea Party, Obama, global warming)

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program for filtering and trimming data
by Joanne Rampersad 10 Jun '11

10 Jun '11

Hi Is there an stand alone ( ie not a component of Bowtie etc ) program in galaxy that can filter or trim fastq data? thanks

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substring sequence on coordinate in columns
by Michal Stuglik 10 Jun '11

10 Jun '11

Hi all, I am wondering if galaxy has tool to substring/extract sequence/text from another sequence/text based on coordinates in columns (start, end column) or how to do it in Text Manipulation/Compute? all the best, michal

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Converting transcriptomes to proteomes
by David Matthews 09 Jun '11

09 Jun '11

Dear Galaxy users, I am trying to modify the human proteome based on my transcriptomeics data. In short I want to use my transcriptomics data to identify snps and from that identify coding changes that result from the snps. Ultimately I'd like to create a customised canonical proteome based on my transcriptomic data. Does anyone know how this might be done in Galaxy? I have started by running a pileup and so on but I am not a human geneticist (I am a virologist) so I may be making some fundamental errors!! Any help is gratefully received! Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews(a)bristol.ac.uk

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Galaxy tool error report from johnwu@ibms.sinica.edu.tw
by galaxy-user＠lists.bx.psu.edu 09 Jun '11

09 Jun '11

GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "192.168.0.36:8080" ----------------------------------------------------------------------------- This is in reference to dataset id 377 from history id 2 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 176: Cuffcompare on data 175: transcript accuracy by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. 192.168.0.36:8080/history/view?id=f597429621d6eb2b ----------------------------------------------------------------------------- The user 'johnwu(a)ibms.sinica.edu.tw' provided the following information: While executing cuffcompare, I encountered this error message: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' I was practicing RNA-seq analysis steps on newly installed galaxy to test if i could easily analyze my data. I could run cufflinks and cuffdiff through galaxy, but i'm unable to run cuffcompare. how should i solve this problem? thanks a lot! ----------------------------------------------------------------------------- job id: 126 tool id: cuffcompare ----------------------------------------------------------------------------- job command line: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py -s --ref_file="None" --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data /home/galaxy/software/galaxy_dist/database/files/000/dataset_376.dat ----------------------------------------------------------------------------- job stderr: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' ----------------------------------------------------------------------------- job stdout: cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -s /home/galaxy/data/galaxy_data/sam_index/hg19.fa ./input1 ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).

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Aligning against Multiple Reference Sequences
by John David Osborne 09 Jun '11

09 Jun '11

Are there any tools in Galaxy to align short reads against multiple reference sequences? I have a dozen microbial genomes sequenced for which there are 2 reference genomes already sequenced. We have tried aligning each of these individually against either of the reference genomes - some align better against the first reference genome, some align better against the second reference genome. Ideally though I would like to be able to align against both at the same time. Is this possible? I have found a tool called GenomeMapper and hints of 2 other tools in development that do something like this, but nothing for Galaxy yet. How do others proceed with this type of problem? Workflows appreciated! :) -John

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Cufflinks error in galaxy
by 吳正華 09 Jun '11

09 Jun '11

Hi galaxy dev team: I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis according to Jeremy's excellent tutorial http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise however, I encountered following error messages when I was trying to execute Cufflinks in galaxy.. Dataset generation errors Dataset 121: Cufflinks on data 92: gene expression Tool execution generated the following error message: Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' The tool produced the following additional output: cufflinks v1.0.3 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4 -b how should I solve this problem? Thanks in advance. Best Regards, John Wu

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