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

setting environment for sge scripts
by Andreas Kuntzagk 15 Apr '10

15 Apr '10

Hi, I followed the advice for multiple installed python versions to set ~galaxy/galaxy-python/python and set the environment for the galaxy user to have that in the PATH Problem is, when a job is started on GridEngine, it does not use the "-V" flag to inherit the environment. So it runs with a different python version and more important it does not set LD_LIBRARY_PATH and fails for some tools which need some special lib. (libRblas in this case) Where can I fix that? regards, Andreas

4 6

Suggestion on functionality for published workflows
by Timothy Hughes 12 Jan '10

12 Jan '10

I have heard from jgoecks <http://bitbucket.org/jgoecks/> that the galaxy team are working on a repository for all galaxy objects. I would like to suggest that all workflows that are shared publically (published) have a mandatory field that briefly describes their functionality and that the repository have search functionality which enables a search of published workflows using this field. I am sure their are loads of great workflows out there which are either immediately usable or are easily adaptable. Getting access to such workflows would also be an excellent way to learn Galaxy in a complementary way to the screencasts. While we are waiting for such functionality, perhaps Galaxy developers could set up a simple page where the public histories / workflows can be posted. The simplest solution might be just a check box on the sharing page ("post link to publicly accessible page"), alternatively just a piece of text on the sharing page encouraging users to manually post on specific forum or mailing list. Tim. -- Tim Hughes PhD (http://digitised.info) Medical Genetics Department Oslo University Hospital Ullevål Kirkeveien 166 0407 Oslo Norway

3 2

Fetching promoters
by Linda Barnum 08 Jan '10

08 Jan '10

Hello, Is there a way to fetch the promoter regions for homologous genes from different species. E.g. say I'd like to fetch the promoter region for a drosophila gene CG13222 from drosophila as well as its CG13222 homologues in other flies from UCSC genome browser? Thanks, Lin

3 2

reduced datasets
by Douglas Rhoads 25 Dec '09

25 Dec '09

In the Metagenomic Analysis tutorial they used a reduced dataset to speed things up. I am going to be using Galaxy as part of my hands-on Genomics and Bioinformatics course. In the lab portion, students (20-30) will be doing their own analyses. If everyone is trying to do a full dataset on the Windshield Splatter we will never get done with the Megablast. Is there a simple way, maybe using Galaxy to reduce the size of the 454 data and QV? Even if I have to make the reduced data sets myself.

2 1

Reduced Dataset
by drhoads＠uark.edu 25 Dec '09

25 Dec '09

In the Metagenomic Analysis tutorial they used a reduced dataset to speed things up. I am going to be using Galaxy as part of my hands- on Genomics and Bioinformatics course. In the lab portion, students (20-30) will be doing their own analyses. If everyone is trying to do a full dataset on the Windshield Splatter we will never get done with the Megablast. Is there a simple way, maybe using Galaxy to reduce the size of the 454 data and QV? Even if I have to make the reduced data sets myself. Douglas Rhoads, Professor of Biological Sciences Director of Graduate Program in Cell and Molecular Biology 601 SCEN, Dept. of Biological Sciences, 1 University of Arkansas, Fayetteville, AR 72701 drhoads(at)uark.edu, http://biscweb.uark.edu/drhoads phone: 479-575-3251 FAX: 479-575-4010

1 0

Re: [galaxy-user] Fetching promoters
by Anton Nekrutenko 25 Dec '09

25 Dec '09

Yes. This will be happening shortly. a. On Dec 25, 2009, at 1:14 PM, Linda Barnum wrote: > is there any plan to update the dm2 build to dm3 in Galaxy? Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org

1 0

Dataset visivility policy
by MORITA Hideyuki 24 Dec '09

24 Dec '09

Hi, In Galaxy demonstrated now, everyone can see data, if they can know URL. (e.g. http://main.g2.bx.psu.edu/datasets/**********/display/) A user can set the permission to the dataset with "edit attibutes". However, it is not effective for above-mentioned URL. I am expecting as default function that only I can see the data that I made. And, I think it is insufficient only to make it to a difficult forecast of the ID part of URL. Please tell me your policies concerning the data visibility. And, do you have the plan to implement the function that I expect it? Thanks. MORITA Hideyuki.

2 2

paster.log location
by Erick Antezana 22 Dec '09

22 Dec '09

Hi, is there a way to define in the "universe_wsgi.ini" the location of my log file "paster.log" ? cheers, Erick

2 3

GALAXY Question
by Hadzic, Tarik 21 Dec '09

21 Dec '09

Hello, I was wondering if you could help figure out how to download sequences of all first introns in the fly genome? I've been dabbling in the dark and the tutorials haven't helped me, at least not so far. Thanks, Tarik The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 1

miRNA
by Angela V. Vitale 21 Dec '09

21 Dec '09

Hi, Is there an easy way to compare miRNA files to mm9 if the files are bed files, or do they need to be in fasta format? Sorry, but I've gone through the tutorials and am am a bit confused. Angela

2 1