February 2011 - galaxy-dev - lists.galaxyproject.org

installation and configuring galaxy
by Pauras P Patil 17 Feb '11

17 Feb '11

Hello, I am currently working on a project related to bioinformatics here at Purdue University and we wanted a tool that could create a workflow for the data that we collect. I have downloaded the source code for galaxy, but have no idea on how to integrate galaxy with our website. Could you please give me some steps on how to go about doing that. Thank You Pauras Patil Purdue University | Computer Science

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Configuration of galaxy, metada values are missing
by Christian Dreischer 17 Feb '11

17 Feb '11

Hello community, I'm new to Galaxy and are currently trying to install a new instance on a debian system. So far I installed postgres and created a user and a database for galaxy. In the universe_wsgi.ini file I did the recommended changes and set this entry: database_connection = postgres:///galaxydb?host=/var/run/postgresql for the connection to postgres. For test purposes I uploaded the test file from http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt. After uploading the file I get a warning that "required metadata values are missing". Auto-detect doesn't help. Since it all works fine with sqlite, I assume an incorrect configuration of the postgres user and|or a missing or false entries in pg_hba.conf or universe_wsgi.ini. Thanks in advance for any suggestions Christian

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best practice for data matrices with metadata
by Keith Sheppard 17 Feb '11

17 Feb '11

Hi All, I'm working on building some galaxy tools which can be used together in a workflow and one data structure that seems to show up a lot is a data matrix where both the data rows and data columns have annotations which I would like to preserve through the workflow. Here is an example that hopefully make this more concrete: we have X genotyping probes in a microarray that we have run on Y samples which results in a data matrix with X rows and Y columns. Each of the probes (rows) has annotation data like allele (A vs B allele), sequence, SNP ID, etc and each of the columns (samples) has it's own annotation data like strain, date etc... So what do you think is the best way to represent this kind of structure? Does galaxy have a mechanism that allows you to associate files as a logical group which would allow my intensity data and meta data to stay together as a "dataset" without having to be in the same file? Thank you Keith

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Re: [galaxy-dev] [galaxy-user] Filename extension in new tool
by Peter Cock 17 Feb '11

17 Feb '11

On Thu, Feb 17, 2011 at 3:00 AM, Sean Davis <sdavis2(a)mail.nih.gov> wrote: > I have a tool that takes a pdb file as input. The authors of the *compiled* > code require that the suffix be either ".pdb" or ".ent". When I upload a > .pdb file, the filename that gets fed to the tool now ends in .dat. What is > the best way to get the original file extension stored in the file database? > > Thanks, > Sean Once in Galaxy all the data files have the extension .dat on disk, so I would try using a wrapper script that creates a symbolic link from the input.dat file to something like input.pdb or input.ent (and if that doesn't work, copy the file) before running the compiled code and then remove it afterwards. Separately from this, you may need to extend Galaxy to define pdb as a new file format (ideally with a data type sniffer). This kind of question is better asked on the dev list (CC'dd) Peter

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Galaxy Project on Twitter
by Dave Clements 16 Feb '11

16 Feb '11

Hello all, The Galaxy project is now posting relevant news items on Twitter, starting about a week ago. I don't expect this to initially reach a large volume, somewhere between 0 and 3 tweets per day, but the volume may increase over time. If you are interested, please follow *galaxyproject*. We are tagging all posts specifically about Galaxy with the *#usegalaxy*hash tag. Please use that tag in any Galaxy related posts you make. In the near future we'll post a twitter feed on the main Galaxy landing page, and we'll also announce this on the galaxy-user list. Please let me know if you have any questions, Thanks, Dave C PS: And there are only 2 days left to submit an abstract to the Galaxy Community Conference: http://galaxy.psu.edu/gcc2011/Abstracts.html -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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megablast and blastdb
by David Hoover 16 Feb '11

16 Feb '11

When I try to load the megablast_wrapper tool, I get errors in the output: AssertionError: Data table named 'blastdb' is required by tool but not configured I am totally confused how blastdb.loc should be configured. Is it one tab, two, three? David Hoover Helix Systems Staff http://helix.nih.gov

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Percent and pipe sign in text input fields
by Bossers, Alex 16 Feb '11

16 Feb '11

Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or "%f" it returns Xf or "Xf" in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is "XgXXaXXt". So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex

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New install problem
by Ryan Golhar 16 Feb '11

16 Feb '11

Hi - I'm running CentOS 5.5. My version of python is: [root@genomes ~]# which python /usr/bin/python [root@genomes ~]# python -V Python 2.4.3 I just downloaded galaxy to run a local instance using: hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist and then tried to run it using 'sh run.sh'. When I do so, galaxy proceeds to download eggs that are out of date. After doing some fetching, I see: One or more of the python eggs necessary to run Galaxy couldn't be downloaded automatically. You can try building them by hand (all at once) with: python scripts/scramble.py Or individually: python scripts/scramble.py python_daemon Fetch failed. What does this mean?

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percent and pipe sign in text input fields
by Bossers, Alex 16 Feb '11

16 Feb '11

Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or "%f" it returns Xf or "Xf" in the the variable. For single field lines I solved it to remove the % from the argument and only add it at command line, but in this case it can contain % signs anywhere... For instance %g|%a|%t should return by the tool gi..|accno|title. However the variable returned by the tool xml is "XgXXaXXt". So it also masks the | (pipe) sign... How to solve this? Thanks for any help. Alex

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Data Library Upload Issues
by SHAUN WEBB 15 Feb '11

15 Feb '11

Hi, I have notice a few problems which may or may not have been fixed in the latest distribution (I am yet to update) but wanted to make you aware. 1. Non-admin users with add permissions on a library are offered the option to upload from file systems path. Should this be restricted to admin users only? 2. If a user chooses the option "upload a directory of files" but does not have a folder with their username in the library upload directory they get a server error. Would be nicer to get a help message that says they are not set up for this method and to contact the Galaxy admin. 3. If files are being uploaded to a library and I click on the manage jobs tab in the admin section I get a server error. This persists until the server is restarted. Thanks for your help! Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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