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
12 years, 5 months
purging deleted datasets
by Erick Antezana
Hi,
how can I purge my deleted datasets that were imported so that I could
clean a bit my disk? I saw they are under database/files/000/*
thanks,
Erick
12 years, 9 months
Collecting User Information on the Registration page
by lentaing＠jimmy.harvard.edu
Hi,
We are interested in collecting more information about the user, e.g.
which lab they're part of etc, as they register to use our local mirror of
galaxy. Is there an easy way to add these fields to the registration
page; is it also easy to store these values to the (galaxy) database?
Thanks!
Len
12 years, 10 months
Using mysql instead of sqlite
by Erick Antezana
Hello,
I would like to use MySQL instead of sqlite to store my data. I coudn't
find on the Galaxy web site a HOWTO or some guidelines to do it. I only
found some lines that might need to be changed/enabled in the
universe_wsgi.ini file:
#database_file = database/universe.sqlite
database_connection = mysql:///galaxy
#database_engine_option_echo = true
#database_engine_option_echo_pool = true
#database_engine_option_pool_size = 10
#database_engine_option_max_overflow = 20
Could you point out to some doc or briefly describe what I need to do in
order to go for mysql?
Are there any plans to support other DBMS's (like Oracle for instance)?
thanks,
Erick
12 years, 11 months
Default global variables in Galaxy
by gerrit
Hi there,
Can anyone tell where I can find a description of the default global
variables in Galaxy. From the tool examples I can gather that
GALAXY_DATA_INDEX_DIR is one but can not find documentation of any other.
Thanks,
Gerrit
12 years, 11 months
Experience with Loading NGS data on standalone instance of galaxy
by Abhishek Pratap
Hi All
I recently came to know about NGS analysis on galaxy during ISMB.
Getting excited I tried couple of things basically to play with it.
Few comments : I may have interepretted something described below in a
wrong way. My apologies before hand.
On a standalone installation of galaxy while I was trying to explore
one FASTQ(sequence) file. It takes considerable (> 20 min) for a fastq
file to get uploaded (2 GB). I am not sure what is the rationale
behind that. Ideally I think there should be no need to upload such
heavy files into the workspace. They could actually be used straight
away by the path specified. Also is there any way to access the
scripts for analysis on the command line. I know this undermines the
main aim of working with galaxy but rite now I am concerned about the
performance/time.
I will be happy to discuss more about this in case you have some
comments/questions for me.
Best,
-Abhi
-----------------------------
Abhishek Pratap
Bioinformatics Software Engineer
Institute for Genome Sciences
School of Medicine, Univ of Maryland
801, W. Baltimore Street, Baltimore, MD 21209
Ph: (+1)-410-706-2296
www.igs.umaryland.edu/
12 years, 11 months
Need Help
by Sonali Jha
Dear Galaxy Team,
I have successfully installed Galaxy and have couple of questions.
(1) How to Change User in Galaxy
(2)How to create user
(2) How data is stored
(3)Where to put Galaxy files for automatic start
I would appreciate your response.
Regards
-Sonali
12 years, 11 months
TopHat to NGS toolbox
by Rathi Thiagarajan
Hello there,
I was really pleased to see that you have the NGS toolbox within Galaxy. I
was wondering if there are any plans to include TopHat
(http://tophat.cbcb.umd.edu/)and/or Cufflinks
(http://cufflinks.cbcb.umd.edu/) into the toolbox as this would be really
beneficial.
Also do you have tools to convert fastq format to SAM?
Thanking you in advance.
Cheers,
Rathi
--
Rathi Thiagarajan
Institute for Molecular Bioscience
University of Queensland, St. Lucia, QLD 4072
AUSTRALIA
12 years, 11 months
galaxy passing an incorrect directory to a script...
by Nick Schurch
I'm having a problem with a script in galaxy.
In the xml config file for the tool I have an html output file defined by
<outputs>
<data name="webpageout" format="html" />
</outputs>
I then use $webpageout.files_path to pass to the script the location
where galaxy is putting the files the script creates. My webpage
contains a link for downloading a postscript file that is created by
the script and the correct path is needed or the download link doesn't
work.
Here at Dundee University we have a 'development' galaxy install and a
'live' galaxy install. Both are the same version and run off the same
mysql database. When I run the script on the 'develpment' version the
script works fine - $webpageout.files_path passes the correct
directory to the script and the script can manipulate the file and
link to it correctly. Unfortunately, when run on the 'live' version
the script throws an error. It appears that galaxy is passing the
script an incorrect directory path through $webpageout.files_path. The
path it passes the script looks something like
/galaxy_live/database/job_working_directory/604/dataset_615_files, but
when I look for the files manually they are actually in
/galaxy_live/database/files/000/dataset_615_files/ .
Does anyone have any idea why galaxy would pass a 'working directory'
to the script rather than the directory where the files are actually
stored? Is it that galaxy actually creates the files in the working
directory and then moves them?
I'm also really confused as to why the 'development' installation
works fine, but the 'live' installation throws this error. Any insight
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
12 years, 11 months
Call galaxy workflows as web service (or cmd line)?
by John Major
I have a local install of Galaxy, and it would be very helpful if I could
leverage Galaxy to help automate some analysis pipelines. Specifically via
a web service'y interface (command line would work too).
This does not appear possible in the current version, but It seems many
features are enabled but not documented yet, so thought I'd check here. If
it is in development, I'd be interested in helping out.
Thanks!
John
12 years, 11 months
