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

Velvetoptimiser error
by Makis Ladoukakis 20 Dec '11

20 Dec '11

Dear Galaxy users, Has anyone worked with velvetoptimiser tool from the Tool shed? I have been trying both the stable and the test version of the velvetoptimiser tool and i keep getting the same error: Traceback (most recent call last): File "/home/ladoukef/galaxy_dist/tools/myTools/velvetoptimiser/velvet_optimiser.py", line 102, in if __name__ == "__main__": __main__() File "/home/ladoukef/galaxy_dist/tools/myTools/velvetoptimiser/velvet_optimiser.py", line 67, in __main__ for line in open(contigs_path ): IOError: [Errno 2] No such file or directory: 'contigs.fa' Can someone identify where the error is? The file missing (contigs.fa) is supposed to be built by the tool itself. Thank you, Efthymios Ladoukakis

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Workflows & Multiple datasets
by Adhemar 19 Dec '11

19 Dec '11

Hi, I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well? I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'? Thank you, Adhemar

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Tophat jobs not starting
by Magdalena Strzelecka 19 Dec '11

19 Dec '11

Hi, I have submitted some jobs to Tophat, but they have not started since yesterday (Dec 13th); i.e they were in a queue for >12 hrs. I have re- submitted everything again (2 jobs), but the same situation is happening. Is there some issue with Tophat at the moment? Thanks. M. ------------------------------ Magdalena Strzelecka, PhD Heald Lab University of California, Berkeley Department of Molecular & Cell Biology 315 Life Sciences Addition # 3200 Berkeley, CA 94720-3200 phone: (510) 643-5002 fax: (510) 643-6791 e-mail: strzelecka(a)berkeley.edu

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Finding Galaxy version
by Paul-Michael Agapow 19 Dec '11

19 Dec '11

A perhaps obvious question: how do I work out what version of Galaxy an instance is? This has come up a few times because of apparent bugs and different behaviour across various development and production instances. Now if you're installed straight from the repo, you can use "hg log" for the repo number. But that doesn't work if it's been installed in another way, say from a tarball or via another versioning system (we use git to synchronize tool development to a production server). Simple solution? ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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comparing data sets with different coordinates
by dvera＠bio.fsu.edu 18 Dec '11

18 Dec '11

Hello, May I use galaxy to do correlation analyses with two continuous quantitative data sets containing different coordinates (two different microarray designs)? How can I create sliding windowed averages for these data sets to accomplish this? How can I perform a correlation analysis with a wiggle and a bed (e.g., microarray data VS gene density). Would I need to do a grouping of my microarray data with another spreadsheet defining the window coordinates? Thanks, Dan

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Performing operations on tab delimited text files
by Lanelle Oni Edwards 16 Dec '11

16 Dec '11

Hi, My name is Lanelle Edwards. I am a new galaxy user. I uploaded a tab delimited text file to my history. However, the first column of the data I imported is solely chromosome number and start and end position (ALL IN ONE COLUMN) in the format chrI:1000000-2000000. My question is: How can I filter out these values into separate columns using galaxy tools? For example: Having a separate column for chromosome number, column for start position, column for end position. I would really appreciate the help. Thanks, Lanelle Edwards Lab Manger University of Maryland

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(no subject)
by Giuseppe Petrosino 16 Dec '11

16 Dec '11

Hi, I read on Readme for MACS that: "For the experiment with several replicates, it is recommended to concatenate several ChIP-seq treatment files into a single file". Now, I have illumina ChipSeq data: two files for IP samples and two files for Control samples. Is It right to use Concatenate datasets (text manipulation) and then use MACS for the peaks calling? Thank you so much. Giuseppe

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about ftp setting up
by Liao_Ruiqi 15 Dec '11

15 Dec '11

Hello there， I'm a student at Fudan University in China. I was trying to enable ftp uploading in my local version of GALAXY. I tried the setting in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP, but I got the following problems: 1. The galaxyftp seems to be a pasql database, shall I build it myself? or dose it already exists in galaxy directory? 2. the galaxy_user seems to be a table, shall I build it myself? and how shall I update it and integrate it with galaxy? Thanks for your attention, and looking forward to your reply! Best wishes Liao Ruiqi

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Extract genomic DNA
by Rebecca C Mueller 14 Dec '11

14 Dec '11

Hi all, Does anyone know if you can use the "Extract Genomic DNA" command with a genome not in the database? I am working with an algal genome (C. merolae) that isn't currently in the pulldown Database/Build menu. I keep getting the "Unspecified genome build" error, and am assuming that's the problem, as my other files appear to be formatted correctly (tab delimited without spaces for the intervals, same names for chromosomes in interval and fasta file, etc). Thanks! Rebecca

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Looking for Galaxy related papers (or have written one)? There is a new Galaxy Group @ CiteULike
by Dave Clements 14 Dec '11

14 Dec '11

Hello all, A new Galaxy Group <http://www.citeulike.org/group/16008/order/group_rating>has been created at the CiteULike <http://citeulike.org/> social bookmarking service to organize papers that are about, use, or reference Galaxy. The Galaxy Group<http://www.citeulike.org/group/16008/order/group_rating>is open to any CiteULike user (and anyone can become a CiteULike user). Group members can add papers to the group, assign tags, and rate papers. CiteULike makes extensive use of *tags* to organize and categorize papers. The Galaxy group uses this set of tags<http://wiki.g2.bx.psu.edu/CiteULike#CiteULike_Tags>to categorize papers. If you want to help other Galaxy users and sites find papers that are relevant to them, or help the Galaxy Project keep track of what papers (and communities) are using Gaalxy, then please help by adding relevant papers to the Galaxy Group Library<http://www.citeulike.org/group/16008/order/group_rating>and/or rating and tagging the papers that are there. *We particularly need help with papers that were published before this year, as very few of them are in the initial list. * Links: http:/galaxyproject.org/wiki/CiteULike - Explanation of tags http://www.citeulike.org/group/16008/order/group_rating - Galaxy Group list of papers Thanks, Dave Clements PS: To cite the Galaxy Project, see http://galaxyproject.org/wiki/Citing%20Galaxy. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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