- galaxy-user - lists.galaxyproject.org

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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Re: [galaxy-user] Fwd: starting workflows with a pool of input files
by Matthias Dodt 12 Oct '09

12 Oct '09

Okay Thanks;-)! greetings mat Dominic Tolle schrieb: > fyI > > Begin forwarded message: > >> *From: *Greg Von Kuster <ghv2(a)psu.edu <mailto:ghv2@psu.edu>> >> *Date: *October 8, 2009 3:34:35 PM GMT+02:00 >> *To: *Matthias Dodt <matthias.dodt(a)mdc-berlin.de >> <mailto:matthias.dodt@mdc-berlin.de>> >> *Cc: *galaxy <galaxy-user(a)bx.psu.edu <mailto:galaxy-user@bx.psu.edu>> >> *Subject: **Re: [galaxy-user] starting workflows with a pool of input >> files* >> >> Hello Matthias, >> >> I've opened the following ticket for this question - you can "follow" >> the ticket in bitbucket if you want. >> >> http://bitbucket.org/galaxy/galaxy-central/issue/197/starting-workflows-wit… >> >> Greg Von Kuster >> Galaxy Development Team >> >> >> Matthias Dodt wrote: >>> Hi there! >>> >>> I would like to start a workflow several times (with a pool of input >>> files). >>> >>> The reason is: >>> Lets say we process huge FASTA files. To do so, i incorporated a >>> splitting tool into our galaxy, which creates several smaller >>> split-files, which can be more easily processed on a cluster in >>> parallel. Now i would like to start a workflow with these splitfiles as >>> input (without starting it manually by clicking lets say 100 times - >>> for >>> each split-file - the same procedure). >>> >>> Is there an easy way to do that? >>> >>> thanks! >>> >>> greetings >>> >>> mat >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)bx.psu.edu >>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user >>> >>> >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)bx.psu.edu >> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user >

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Re: [galaxy-user] Experience with Loading NGS data on standalone instance of galaxy
by Abhishek Pratap 12 Oct '09

12 Oct '09

Hi Greg Based on the testing of the new feature I am not sure if it working as expected. I gave galaxy a path to GERALD folder (which is a analysis folder generated by Illumina pipeline) and selected file type to be just "solexafastq". It took about two hours for the process to be completed. Somehow it went through each file and uploaded everything in the library. Ideally it should look up only the relevant fastq files and upload total of 8 files (1 / lane ) present in the folder. This process should be very fast as it would just record the path. Thanks, -Abhi On Mon, Oct 5, 2009 at 11:37 AM, Abhishek Pratap <abhishek.vit(a)gmail.com>wrote: > I made sure I selected just one file format(fastqsolexa). The path I > gave was to a GERLAD folder. Basically a folder with bunch of analysis > files plus 8 fastq files. I would say it is still taking a long time > to put the path of only 8 fastq files in question to galaxy system. > > -Abhi > > On Mon, Oct 5, 2009 at 11:21 AM, Greg Von Kuster <ghv2(a)psu.edu> wrote: > > This logging looks correct. I replied to your previous message: > regarding > > this issue, are you setting the datatype manually or allowing for > > "auto-detect"? Manually setting the datatype would probably be a good > idea > > to speed things up. If not all files being uploaded are of the same > type, > > pick one and then fix the others later using the "Edit this dataset's > > information" feature. > > > > > > Abhishek Pratap wrote: > >> > >> Hi Greg > >> > >> I hope you had a good weekend. Carrying on from where we left it. I am > >> not able to get to the required page from where I believe I should be > >> able to upload datasets without them getting copied to galaxy > >> filepath. > >> > >> This is what I did > >> > >> 1. Admin -> Data -> Manage Data Libraries > >> 2. Create new data library datasets -> Selected (Upload Files from > >> Filesystem Paths) > >> 3. Pasted the path in the text box > >> 4. Checked the checkbox Copy Data into Galaxy ? NO > >> > >> It is taking very long for the dataset pseudo upload to galaxy > >> filesystem. I can see the following incrementing entries in the log > >> file. Is it the way it is supposed to be ? > >> > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:42,189 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:43,892 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:45,598 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:47,380 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:49,022 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:50,446 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:52,029 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:53,491 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:55,134 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:56,788 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:11:58,433 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:00,112 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:01,752 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:03,712 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:05,525 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:07,235 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:09,062 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:10,864 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:12,914 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:14,567 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:16,240 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> galaxy.tools.actions.upload_common DEBUG 2009-10-05 11:12:18,057 > >> DEBUGDEBUG: In Test_GA_Data_Set, found a folder name match: 8:Temp > >> > >> > >> Thanks, > >> -Abhi > >> > >> > >> > >> On Fri, Oct 2, 2009 at 4:26 PM, Abhishek Pratap <abhishek.vit(a)gmail.com > > > >> wrote: > >>> > >>> I found the error. I had multiple test instance running and I was > >>> using a wrong one to see the changes. My bad. > >>> > >>> -A > >>> > >>> On Fri, Oct 2, 2009 at 4:20 PM, Greg Von Kuster <ghv2(a)psu.edu> wrote: > >>>> > >>>> Hmm...ok, can you attach your universe_wsgi.ini file so I can take a > >>>> look? > >>>> > >>>> > >>>> Abhishek Pratap wrote: > >>>>> > >>>>> I see > >>>>> > >>>>> Analyze Data ¬†Workflow Data Libraries Help User > >>>>> > >>>>> -A > >>>>> > >>>>> On Fri, Oct 2, 2009 at 4:13 PM, Greg Von Kuster <ghv2(a)psu.edu> > wrote: > >>>>>> > >>>>>> What so you see in the top menu bar? > >>>>>> > >>>>>> Do you see this? > >>>>>> > >>>>>> Analyze Data ‚Ä† ‚Ä†Workflow ‚Ä† ‚Ä† ‚Ä† ‚Ä†Data Libraries ‚Ä† ‚Ä† > ‚Ä† > >>>>>> ‚Ä† ‚Ä†Admin ‚Ä† ‚Ä†Help > >>>>>> > >>>>> > >>>> > >> > >> > > > > >

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Registering new users/Datalibraries
by Matthias Dodt 08 Oct '09

08 Oct '09

Hi there! Did anybody gain any experience with this: 1. Is it possible to let the administrator manually confirm each user that registers before he can log into galaxy? 2. We would like to have different Administrators: - for managing users and libraries - for managing (creating) only new libraries and assigning users As i can see so far it is not possible to assign any specific permissions to roles? thanks for any hint! greetings mat

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Password as input parameter
by Jelle Scholtalbers 08 Oct '09

08 Oct '09

Hi, is there a possibility to have the type 'password' in the input parameter section? So that the password the user is typing is not shown on screen? Considering users and passwords, can I use user information (from a user that is logged in) in my tool configuration files? Cheers, Jelle

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