May 2010 - galaxy-user - lists.galaxyproject.org

Galaxy + SGE
by Erick Antezana 07 May '10

07 May '10

Hi, I just installed and configured Galaxy to run on our SGE cluster. I tried to upload a file (fasta, ggff3, ...) without any success... it seems I missed something at the level of the config. the log shows the following message: galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create any tip where to look at? I am making use of the proxy config too (http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy) which actually works very fine in our other instances that are running on local (not clustered). thanks, Erick

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D Mel reference genome for mapping
by Farhat Habib 07 May '10

07 May '10

Dear Galaxy devs, Would it be possible to include drosophila Melanogaster (dm3) genome for mapping in NGS toolbox? D Mel is a widely used model organism and I am sure many biologists could use it. Thanks, -Farhat -- Farhat Habib, PhD IISER Fellow, Biology Indian Institute of Science Education & Research, Sai Trinity Building, Garware Circle, Sutarwadi, Pashan, Pune-411 021. http://www.iiserpune.ac.in/~farhat Office: +91 20 2590 8015 Cell: +91 973 0996 233

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Undelete
by Steve Taylor 06 May '10

06 May '10

Hi, If I accidentally delete a output from a history is it possible to undelete it? Kind regards and thanks, Steve

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Load Balancing
by Erick Antezana 06 May '10

06 May '10

Hi, where can I find some more info/docs about 'load balancing' in Galaxy? it seems that the right place is: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/LoadBalancing as indicated in the universe_wsgi.ini (enable_job_running). cheers, Erick

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Custom java tool
by Nils Homer 06 May '10

06 May '10

What is the best way to include wrap a JAR file in galaxy? Also, what is the best way to submit tools and their associated wrappers? Thank-you for your help in advance, Nils Homer

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server error
by Keith Giles 06 May '10

06 May '10

I'm getting a server error for every operation that I'm trying. Its telling me to turn on "debug" to see what the problem is, but I can't find where to do that. Is anyone else having (or have had) this problem?

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Database schema
by Nils Homer 05 May '10

05 May '10

Could someone point me to the documentation for the sql-lite schema used in Galaxy? I would like to set up a mysql database and I am looking for instructions on how to get it working with Galaxy with the correct schema. Sincerely, Nils Homer

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STRAND info in the second query is NOT recognized by "interval INTERSECTION"
by Xianjun Dong 05 May '10

05 May '10

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Setting line 1 of file to be a header
by Shraddha Pai 05 May '10

05 May '10

Hi, Is there way to have the first row of a data file to be set as being a header? ie so that the names are taken out of the data file, included in the blue column header table, and stay with the datafile through simple transformations (e.g. filtering)? If not exactly that, is there some way to keep the header labels with the data file without it interfering with analysis? Thanks in advance, Shraddha ----- Shraddha Pai Post-doctoral fellow, Petronis lab Krembil Family Epigenetic Research Laboratory Centre for Addiction and Mental Health, Toronto ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________

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MACS input format
by Steve Taylor 05 May '10

05 May '10

Hi, What format does MACS take as input within Galaxy? Thanks, Steve

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