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
11 years, 4 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
11 years, 5 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
11 years, 5 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/
11 years, 5 months
various import dir's
by Erick Antezana
Hi,
how can I defined various library import directories within the
"universe_wsgi.ini" by using the "library_import_dir" ?
same question for "user_library_import_dir"?
thanks,
Erick
11 years, 7 months
headers in tabular datatypes
by James Casbon
Deaf galaxy-user,
So you can have tabular datasets, and you can add a datatype that
subclasses tabular and adds column definitions.
Is there a way of using tabular data with column headings without
defining the datatype, i.e. getting galaxy to recognise that first
line is a header and should be used as column titles?
thanks,
James
11 years, 7 months
New local Galaxy Install: Problem with grouping -- rpy issue
by Hans Vasquez-Gross
Hello All,
When running a grouping on a data set via the Join, Subtract, Grouping
menu, I receive this error.
An error occurred running this job: *Traceback (most recent call last):
File "/opt/Bio/galaxy_dist/tools/stats/grouping.py", line 7, in ?
from rpy import *
ImportError: No module named rpy
*I'm having the hardest time figuring out which R version with what version
of Rpy to use. So far I've tried rpy-1.0.3, rpy2-2.0.6, with Rpackages
2.7.2 and 2.9.1. I've gotten both rpackages to compiled with the
--enable-R-shlib option and I have put it in my $PATH. However, when trying
to install either of they rpy packages, they complain about missing header
file RGraphics.h, Rdevices.h, and more. Does anyone have a known good
configuration to get this module working with galaxy? Which R package with
which rpy version should I be using?
Thanks,
Hans Vasquez-Gross
11 years, 7 months
Tutorial for making workflow
by Bagdevi
Hello All,
I am new to GALAXY. I tried to make a functional workflow but could
not succeed. Can anybody tell me, where can I find the tutorial for
the preparation of workflow.
Regards,
Bagdevi Mishra.
11 years, 7 months
other genomes
by Eric Rivals
Dear Galaxy team,
i would like to work on a few genomes that do not seem to be available
on the system. Is it possible, and if yes how can i integrate those on
Galaxy?
sincerely yours,
Eric
Le 21 août 09 à 18:00, galaxy-user-request(a)bx.psu.edu a écrit :
> Send galaxy-user mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of galaxy-user digest..."
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>
> Today's Topics:
>
> 1. Re: Passing a string with spaces to a tool (Nick Schurch)
> 2. Re: Passing a string with spaces to a tool (James Casbon)
> 3. Re: Passing a string with spaces to a tool (Gordon, Assaf)
> 4. Problems with links in webpage output... (Nick Schurch)
> 5. Re: Problems with links in webpage output... (Daniel Blankenberg)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 Aug 2009 10:47:38 +0100
> From: Nick Schurch <N.Schurch(a)dundee.ac.uk>
> Subject: Re: [galaxy-user] Passing a string with spaces to a tool
> To: galaxy-user(a)bx.psu.edu
> Message-ID:
> <cb86364c0908210247m111c58cdv60ac45a1f8e7f775(a)mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Galaxy-gurus,
>
> How can I pass a string with spaces as a parameter from the galaxy
> interface
> to a tool that I've written myself in perl? I've tried enclosing the
> string
> with quotes (single and double) and various escape characters and
> all they
> do is add __dq/sq/X__ to the start of the string and then ignore
> everything else after the space.
>
> my xml looks like:
>
> <tool id="blah" name="mytool">
> <command interpreter="perl">
> /pathto/mycommand.pl -str $str
> </command>
> <inputs>
> <param name="str" type="text" label="Put your string here" />
>
> The kind of commandline i'm looking for this to generate is....
>
> perl mycommand.pl -str "this is my string"
>
> but currently it just gives
>
> perl mycommand.pl -str this
> or
> perl mycommand.pl -str __dq__this
> or
> perl mycommand.pl -str X__dq__this
>
> Thanks!
>
> --
> 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
>
11 years, 7 months
