July 2008 - galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] local sequence storage]
by Greg Von Kuster 12 Sep '08

12 Sep '08

4 3

Galaxy source repository change
by Nate Coraor 06 Aug '08

06 Aug '08

Hello, If you simply use the Galaxy Main or Test sites hosted at PSU, you can safely ignore this message. It pertains to people who've checked out their own copy of Galaxy for development or local use. Galaxy development has recently moved source control systems, from Subversion to Mercurial. This means that anyone using a local copy of Galaxy will need to make some changes to be able to download future updates. The preferred method of obtaining Galaxy source is through Mercurial directly (the 'hg' command): hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist Tarballs are also available via the zip/gz/bz2 links here: http://www.bx.psu.edu/hg And the repository is mirrored in Subversion here: svn co http://www.bx.psu.edu/svn/galaxy galaxy_dist Unfortunately, modifications to local copies of Galaxy will need to be transferred from your old checkout to the new checkout. Please let us know via <galaxy-bugs(a)bx.psu.edu> of any issues. Thanks, and thank you for using Galaxy. --nate

3 3

Importing features from BioMart
by Alexandre Gattiker 04 Aug '08

04 Aug '08

Hello, I would like to import features from BioMart into galaxy. However the 'embedded' BioMart view yields an HTML table. How do I convert that to GFF or BED? Best regards -- -------------------------------------------------------- Alexandre Gattiker Bioinformatics & Biostatistics Core Facility EPFL School of Life Sciences / Faculté des Sciences de la vie FSV http://people.epfl.ch/Alexandre.Gattiker

2 4

Synteny
by Claudio Casola 31 Jul '08

31 Jul '08

Hello, I found Galaxy extremely helpful in the past months and I have an issue that could again be solved using your wonderful platform. I am playing with a bunch of sequences (genome coordinates) from the human genomes that I obtained from some blast searches. I would like to see if these exact sequences are shared by (in synteny with) chimp, orang and macaque. I got MAF blocks from Galaxy and played with them, but I don't see an easy solution. It would be great if you have some suggestion about how to work with synteny using Galaxy, if possible. Thanks a lot! Claudio Casola Postdoctoral fellow, Hahn Lab Department of Biology 1001 East Third Street Bloomington, IN 47405-3700 Indiana University 812-856-7016 ccasola(a)indiana.edu

2 1

Lift-Over update with orangutan assembly
by Claudio Casola 22 Jul '08

22 Jul '08

Hello, Is there any chance to have the orangutan assembly included in the Lift-Over menu any time soon? That would be great! Thanks, Claudio Casola Postdoctoral fellow, Hahn Lab Department of Biology 1001 East Third Street Bloomington, IN 47405-3700 Indiana University 812-856-7016 ccasola(a)indiana.edu

2 1

Interfacing galaxy with a local copy of the UCSC genome browser
by Tim Yu 22 Jul '08

22 Jul '08

hi there, We've just set up a local instance of Galaxy to serve as a framework for adding custom tools. We also have a local server running a copy of the UCSC genome browser with our own data on it. Is there a way to configure Galaxy to interface with our in-house UCSC server, instead of (or in addition to) the central site? Is this, by the way, the approved place to direct such questions? I didn't see an email address for support on the main site or wiki. Thanks! Tim Yu

2 1

How to get output from Galaxy
by i rezwan 02 Jul '08

02 Jul '08

Hi, I am a very new user at Galaxy. I have downloaded the Galaxy and am running it in my computer locally. Actually I am developing a script in python which I want to integrate with Galaxy on TEST basis. I can add the tool and run the program very well by following Galaxy tutorials. But the one problem that I am facing is, I don't know how to get an output from Galaxy. I will prefer to get the output in a text file locally mentioned by user (to make it a bit more user friendly). I have examined through the example .xml file and also seen the galaxy screencast, but still unable to generate an output file for my tool. I'm using browser: mozilla 3.0 and OS: ubunutu linux. Thanks in advance. Regards /Faisal -- Faisal Ibne Rezwan BioComputation Group, Rm # 1E114 Science and Technology Research Institute University of Hertfordshire College Lane Campus Hatfield, AL10 9AB UK Tel +44 (0)1707 286356

2 1