setting environment for sge scripts
by Andreas Kuntzagk
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
10 years, 9 months
Suggestion on functionality for published workflows
by Timothy Hughes
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
11 years
Fetching promoters
by Linda Barnum
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
11 years
reduced datasets
by Douglas Rhoads
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.
11 years
Reduced Dataset
by drhoads＠uark.edu
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
11 years
Dataset visivility policy
by MORITA Hideyuki
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.
11 years
paster.log location
by Erick Antezana
Hi,
is there a way to define in the "universe_wsgi.ini" the location of my log
file "paster.log" ?
cheers,
Erick
11 years
GALAXY Question
by Hadzic, Tarik
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.
11 years, 1 month
miRNA
by Angela V. Vitale
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
11 years, 1 month
