October 2009 - galaxy-user - lists.galaxyproject.org

setting environment for sge scripts
by Andreas Kuntzagk 15 Apr '10

15 Apr '10

Hi, I followed the advice for multiple installed python versions to set ~galaxy/galaxy-python/python and set the environment for the galaxy user to have that in the PATH Problem is, when a job is started on GridEngine, it does not use the "-V" flag to inherit the environment. So it runs with a different python version and more important it does not set LD_LIBRARY_PATH and fails for some tools which need some special lib. (libRblas in this case) Where can I fix that? regards, Andreas

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purging deleted datasets
by Erick Antezana 17 Dec '09

17 Dec '09

Hi, how can I purge my deleted datasets that were imported so that I could clean a bit my disk? I saw they are under database/files/000/* thanks, Erick

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Collecting User Information on the Registration page
by lentaing＠jimmy.harvard.edu 11 Nov '09

11 Nov '09

Hi, We are interested in collecting more information about the user, e.g. which lab they're part of etc, as they register to use our local mirror of galaxy. Is there an easy way to add these fields to the registration page; is it also easy to store these values to the (galaxy) database? Thanks! Len

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Using mysql instead of sqlite
by Erick Antezana 04 Nov '09

04 Nov '09

Hello, I would like to use MySQL instead of sqlite to store my data. I coudn't find on the Galaxy web site a HOWTO or some guidelines to do it. I only found some lines that might need to be changed/enabled in the universe_wsgi.ini file: #database_file = database/universe.sqlite database_connection = mysql:///galaxy #database_engine_option_echo = true #database_engine_option_echo_pool = true #database_engine_option_pool_size = 10 #database_engine_option_max_overflow = 20 Could you point out to some doc or briefly describe what I need to do in order to go for mysql? Are there any plans to support other DBMS's (like Oracle for instance)? thanks, Erick

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Default global variables in Galaxy
by gerrit 04 Nov '09

04 Nov '09

Hi there, Can anyone tell where I can find a description of the default global variables in Galaxy. From the tool examples I can gather that GALAXY_DATA_INDEX_DIR is one but can not find documentation of any other. Thanks, Gerrit

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Experience with Loading NGS data on standalone instance of galaxy
by Abhishek Pratap 04 Nov '09

04 Nov '09

Hi All I recently came to know about NGS analysis on galaxy during ISMB. Getting excited I tried couple of things basically to play with it. Few comments : I may have interepretted something described below in a wrong way. My apologies before hand. On a standalone installation of galaxy while I was trying to explore one FASTQ(sequence) file. It takes considerable (> 20 min) for a fastq file to get uploaded (2 GB). I am not sure what is the rationale behind that. Ideally I think there should be no need to upload such heavy files into the workspace. They could actually be used straight away by the path specified. Also is there any way to access the scripts for analysis on the command line. I know this undermines the main aim of working with galaxy but rite now I am concerned about the performance/time. I will be happy to discuss more about this in case you have some comments/questions for me. Best, -Abhi ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/

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Need Help
by Sonali Jha 30 Oct '09

30 Oct '09

Dear Galaxy Team, I have successfully installed Galaxy and have couple of questions. (1) How to Change User in Galaxy (2)How to create user (2) How data is stored (3)Where to put Galaxy files for automatic start I would appreciate your response. Regards -Sonali

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TopHat to NGS toolbox
by Rathi Thiagarajan 22 Oct '09

22 Oct '09

Hello there, I was really pleased to see that you have the NGS toolbox within Galaxy. I was wondering if there are any plans to include TopHat (http://tophat.cbcb.umd.edu/)and/or Cufflinks (http://cufflinks.cbcb.umd.edu/) into the toolbox as this would be really beneficial. Also do you have tools to convert fastq format to SAM? Thanking you in advance. Cheers, Rathi -- Rathi Thiagarajan Institute for Molecular Bioscience University of Queensland, St. Lucia, QLD 4072 AUSTRALIA

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galaxy passing an incorrect directory to a script...
by Nick Schurch 20 Oct '09

20 Oct '09

I'm having a problem with a script in galaxy. In the xml config file for the tool I have an html output file defined by <outputs> <data name="webpageout" format="html" /> </outputs> I then use $webpageout.files_path to pass to the script the location where galaxy is putting the files the script creates. My webpage contains a link for downloading a postscript file that is created by the script and the correct path is needed or the download link doesn't work. Here at Dundee University we have a 'development' galaxy install and a 'live' galaxy install. Both are the same version and run off the same mysql database. When I run the script on the 'develpment' version the script works fine - $webpageout.files_path passes the correct directory to the script and the script can manipulate the file and link to it correctly. Unfortunately, when run on the 'live' version the script throws an error. It appears that galaxy is passing the script an incorrect directory path through $webpageout.files_path. The path it passes the script looks something like /galaxy_live/database/job_working_directory/604/dataset_615_files, but when I look for the files manually they are actually in /galaxy_live/database/files/000/dataset_615_files/ . Does anyone have any idea why galaxy would pass a 'working directory' to the script rather than the directory where the files are actually stored? Is it that galaxy actually creates the files in the working directory and then moves them? I'm also really confused as to why the 'development' installation works fine, but the 'live' installation throws this error. Any insight would be greatly appreciated. -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893

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Call galaxy workflows as web service (or cmd line)?
by John Major 16 Oct '09

16 Oct '09

I have a local install of Galaxy, and it would be very helpful if I could leverage Galaxy to help automate some analysis pipelines. Specifically via a web service'y interface (command line would work too). This does not appear possible in the current version, but It seems many features are enabled but not documented yet, so thought I'd check here. If it is in development, I'd be interested in helping out. Thanks! John

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