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

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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SNP finding
by Xiefan Fang 03 Dec '13

03 Dec '13

Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. Thanks, Xiefan University of Florida

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Re: [galaxy-user] Batch jobs...
by Neil.Burdett＠csiro.au 03 Jan '13

03 Jan '13

Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I attach screenshots of what I've got (I have a recent subversion checkout)... Thanks Neil [cid:image001.jpg@01CDB754.FC6C6330] [cid:image002.jpg@01CDB754.FC6C6330]

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Export to file
by Dave Corney 02 Nov '12

02 Nov '12

Hi list, Is there a currently a known problem with the "export to file" function? I'm trying to migrate some data from the public galaxy to a private one; the export function worked well with a small (~100mb) dataset, but it has not been working with larger datasets (>2GB) and I get the error: Server Error. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). Is there a limit on the file size of the export? If so, what is it? Thanks in advance, Dave

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cufflinks visualization
by i b 02 Nov '12

02 Nov '12

Hi all, can anyone explain me wh how can I visualize cufflinks outputs in trackster? galaxy keep sending me errors thanks, ib

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Latest supported Cufflinks?
by Bidwell, Christopher A. 01 Nov '12

01 Nov '12

I am interested in using Cufflinks 2.0 on our local instance of Galaxy but I am not sure if it is supported yet. We did Galaxy update in early October and we tried to install cufflinks V2.0 and it seems to run. I get the output files and they have the genes listed but 0.000 for all results (using files that worked on previous version). The output file summaries contain the following: Info: ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/opt/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/opt/galaxy/galaxy-d Is there a fix for this error or do we need to go back to the latest supported version of Cufflinks and if so which version? Thanks Chris Bidwell

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Using syncing tool in Galaxy
by Sachit Adhikari 31 Oct '12

31 Oct '12

Hello Everyone, I am about to write a syncing tool for Galaxy like Dropbox using Python with the progress bar. How do I integrate it with galaxy? It would be easy for client to upload files using the syncing tool. Are there any syncing tools available for Galaxy? Thanks

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November 2012 Galaxy Update
by Dave Clements 31 Oct '12

31 Oct '12

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Manage libraries permissions with API
by Fabien Mareuil 31 Oct '12

31 Oct '12

Dear all, I would like to know if it is possible to manage libraries permissions with the API galaxy, and how to do that. Thank you for your answer, Best regards, Fabien Mareuil -- Fabien Mareuil | Centre d'Informatique pour la Biologie fabien.mareuil(a)pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux 75015 Paris, France

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sequences for TRAnsfec ids
by shamsher jagat 31 Oct '12

31 Oct '12

This may be a little different question from usual Galaxy use, I have alist of Transfec binding matrix ids -v$1234.... and want to extract bidning sequences corresponding to these ids. Is it possible to extract such sequences with in Galaxy or anyone aware of an alternative approach please. I understand that with genomic coordinates I can extract the sequences in galaxy but I dont see the genomic coordinates. Thanks Kanwar

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