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

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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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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various import dir's
by Erick Antezana 15 Sep '09

15 Sep '09

Hi, how can I defined various library import directories within the "universe_wsgi.ini" by using the "library_import_dir" ? same question for "user_library_import_dir"? thanks, Erick

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headers in tabular datatypes
by James Casbon 01 Sep '09

01 Sep '09

Deaf galaxy-user, So you can have tabular datasets, and you can add a datatype that subclasses tabular and adds column definitions. Is there a way of using tabular data with column headings without defining the datatype, i.e. getting galaxy to recognise that first line is a header and should be used as column titles? thanks, James

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What are the possible computations and what are the commands for "Compute an expression on every row"? Thanks!
by Halfdan Rydbeck 01 Sep '09

01 Sep '09

What are the possible computations and what are the commands for "Compute <http://main.g2.bx.psu.edu/tool_runner?tool_id=Add_a_column1> an expression on every row"? Thanks! Halfdan Rydbeck

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New local Galaxy Install: Problem with grouping -- rpy issue
by Hans Vasquez-Gross 27 Aug '09

27 Aug '09

Hello All, When running a grouping on a data set via the Join, Subtract, Grouping menu, I receive this error. An error occurred running this job: *Traceback (most recent call last): File "/opt/Bio/galaxy_dist/tools/stats/grouping.py", line 7, in ? from rpy import * ImportError: No module named rpy *I'm having the hardest time figuring out which R version with what version of Rpy to use. So far I've tried rpy-1.0.3, rpy2-2.0.6, with Rpackages 2.7.2 and 2.9.1. I've gotten both rpackages to compiled with the --enable-R-shlib option and I have put it in my $PATH. However, when trying to install either of they rpy packages, they complain about missing header file RGraphics.h, Rdevices.h, and more. Does anyone have a known good configuration to get this module working with galaxy? Which R package with which rpy version should I be using? Thanks, Hans Vasquez-Gross

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Tutorial for making workflow
by Bagdevi 26 Aug '09

26 Aug '09

Hello All, I am new to GALAXY. I tried to make a functional workflow but could not succeed. Can anybody tell me, where can I find the tutorial for the preparation of workflow. Regards, Bagdevi Mishra.

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other genomes
by Eric Rivals 25 Aug '09

25 Aug '09

Dear Galaxy team, i would like to work on a few genomes that do not seem to be available on the system. Is it possible, and if yes how can i integrate those on Galaxy? sincerely yours, Eric Le 21 août 09 à 18:00, galaxy-user-request(a)bx.psu.edu a écrit : > Send galaxy-user mailing list submissions to > galaxy-user(a)bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > Today's Topics: > > 1. Re: Passing a string with spaces to a tool (Nick Schurch) > 2. Re: Passing a string with spaces to a tool (James Casbon) > 3. Re: Passing a string with spaces to a tool (Gordon, Assaf) > 4. Problems with links in webpage output... (Nick Schurch) > 5. Re: Problems with links in webpage output... (Daniel Blankenberg) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 21 Aug 2009 10:47:38 +0100 > From: Nick Schurch <N.Schurch(a)dundee.ac.uk> > Subject: Re: [galaxy-user] Passing a string with spaces to a tool > To: galaxy-user(a)bx.psu.edu > Message-ID: > <cb86364c0908210247m111c58cdv60ac45a1f8e7f775(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Galaxy-gurus, > > How can I pass a string with spaces as a parameter from the galaxy > interface > to a tool that I've written myself in perl? I've tried enclosing the > string > with quotes (single and double) and various escape characters and > all they > do is add __dq/sq/X__ to the start of the string and then ignore > everything else after the space. > > my xml looks like: > > <tool id="blah" name="mytool"> > <command interpreter="perl"> > /pathto/mycommand.pl -str $str > </command> > <inputs> > <param name="str" type="text" label="Put your string here" /> > > The kind of commandline i'm looking for this to generate is.... > > perl mycommand.pl -str "this is my string" > > but currently it just gives > > perl mycommand.pl -str this > or > perl mycommand.pl -str __dq__this > or > perl mycommand.pl -str X__dq__this > > Thanks! > > -- > 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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