- galaxy-user - lists.galaxyproject.org

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 06 May '10

06 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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identification of regions
by research pal 05 May '10

05 May '10

Dear Galaxy, First of all let me thank you people for the effort that you are involved in to help the bench scientists world over. I have the ChIP data from ENCODE and I want to see from which part i.e. Exon,Intron or intergenic regions of the human genome they are derived from.In this case can the tools available at galaxy or genome browser help me to reduce my manual efforts ? warm regards, Amit.

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Easy linkage to user dataset files
by Matthew Vaughn 04 May '10

04 May '10

Dear Galactic Overlords, I'd like to be able to provide external access via HTTP GET-able URL to individual data files that are generated in the course of Galaxy analysis. For example, say a user wanted to import her data in Galaxy, do some basic manipulation and then download the resulting data file into another environment using curl or wget... If the user is not authenticated into the Galaxy server (ie is a guest), and she copies the link from a data set in her history by right clicking on the 'Save' icon, she gets something like this: http://main.g2.bx.psu.edu/datasets/259589cb863ac26a/display?to_ext=interval and this URL is retrievable via curl -O "http://main.g2.bx.psu.edu/datasets/259589cb863ac26a/display?to_ext=interval" resulting in a file. However, if the user is coming from an authenticated environment, the link will fail with a Permissions Error from Galaxy. Presumably, this is because the server is checking for presence of a cookie that is set during user authentication. Short of sniffing the authentication token and passing it using curl/wget along with the request (and this will fail when the token expires), is there any way to accomplish what I am asking? Is there a way to provide user credentials via the URL string perhaps? Thanks, Matt == Matthew W. Vaughn, Ph.D. Scientific Lead, iPlant Collaborative Research Assistant Professor Cold Spring Harbor Laboratory 1 Bungtown Road Williams #5 Cold Spring Harbor, NY 11724 USA web: http://hispaniola.cshl.edu/ web: http://www.iplantcollaborative.org/ tel: (516) 367-8808 cell: (516) 353-7055 google-talk: matt.vaughn(a)gmail.com

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