- galaxy-user - lists.galaxyproject.org

create your own importer
by Ido M. Tamir 08 Sep '09

08 Sep '09

http://idotamir.blogspot.com/2009/08/adventures-in-galaxy-pt1.html http://idotamir.blogspot.com/2009/09/adventures-in-galaxy-pt2.html hope this helps. Feel free to ask questions on the blog. best, ido

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new galaxy install hangs
by Ido M. Tamir 08 Sep '09

08 Sep '09

Hi, since two days, when trying a fresh galaxy install it hangs. I don't know if it has to do with my setup or internet connection (fc8, x86_64, Python 2.5.1). hg clone http://bitbucket.org/galaxy/galaxy-central galaxy-central cd galaxy-central after sh setup.sh it stalls at: Creating static/genetrack/plots but after some time it proceeds: One of the python eggs necessary to run Galaxy couldn't be downloaded automatically. You may want to try building it by hand with: python scripts/scramble.py Mako after ./run.sh there is no output for some time, then: Traceback (most recent call last): File "./scripts/paster.py", line 24, in <module> pkg_resources.require( "PasteScript" ) File "/home/tamir/dl/galaxy/lib/galaxy/eggs/__init__.py", line 558, in require if not egg.fetch(): File "/home/tamir/dl/galaxy/lib/galaxy/eggs/__init__.py", line 101, in fetch raise EggNotFetchable( self.name ) galaxy.eggs.EggNotFetchable: PasteScript and this is of course the end of it. best wishes, ido

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When to use metadata or dataset.blurb?
by James Casbon 03 Sep '09

03 Sep '09

So I wanted to add in the number of sequences in a file, which is something that is often requested. My initial thought was to add a tool, which I could do, but then I thought that this was metadata that should probably be added to any record based class. So I then thought that I would find the code that set up the file size information in the history column and copy that, but looking at the source, that goes in the blurb (e.g. sequence.Fasta). So here are my questions: * how can a user see the metadata, as this is distinct to the blurb/peek? * why isn't the file size implemented as a piece of metadata? thanks, James

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use of public server vs local installation
by Jian WJ Wang 01 Sep '09

01 Sep '09

Dear Galaxy team: I was recently introduced to Galaxy framework by my colleagues in Singapore. I am very impressed with it and want to start using it right away. Now the questions are whether I should use the public server or attempt a local installation. I understand this depends on how we intend to use the system. What I would like to get advice from you is the security of using public server. If I setup my login and start using the system for private data, say high throughput sequencing data, who else could possibly see my data without my knowing it? As you know, pharmaceutical companies traditionally have a tendency to setup everything if possible locally. With the recent data explosion, it is becoming more and more unrealistic to maintain internal copies of public tools and data. More importantly, I feel it could be a waste of resource and could introduce unnecessary data provenance problems. From the server maintenance standpoint, how much effort is needed to keep the framework up and running? Do you encourage pharmaceutical companies to use your public server? Have you thought about carving out a section of your server to private users for a fee? I anticipate one or two people to use the server initially for a period of time when we initially get the data and afterwards occasionally use it. I hope to avoid local installation if I possible. Best regards, -Jian _____________________________________________________________ Jian Wang, PhD Informatics Eli Lilly & Co. Phone: 317 655 3496 E-mail: jian.wang(a)lilly.com This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

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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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Problems with links in webpage output...
by Nick Schurch 21 Aug '09

21 Aug '09

Dear Galaxy-gurus, I have a tool I've written myself which runs successfully and generates an HTML file as its output. Included in the webpage are several links for downloading other files produced by the script. I've tried to follow the instructions I found on the wiki -- http://g2.trac.bx.psu.edu/wiki/AddingToolsFAQ -- which gives some (rather vague) instructions about where to put the files and how to reference them in the output webpage, but I'm not having much luck. The script successfully puts the files in the directory where (I think) they are supposed to be: i.e /homes/www-galaxy/galaxy_devel/database/files/000/{myoutputfile}.files_path, and the output links to them very simply with <a href="myfilename.txt">download file</a> - as per the wikipage... But when I view the output webpage from a test run and try and download the links all I get is a page saying: "The resource could not be found. File Not Found (myfilename.txt)." The link itself is pointing to: <my galaxy URL>/datasets/XXX/display/myfilename.txt Is this the right place? Once again, any help 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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