Hello Dave,
Can you clarify how your users are accessing the following URL
http://galaxy.jax.org/user/create
I originally assumed they were using the Galaxy UI to register by clicking the
Register link on the User popup menu. However, perhaps they are just
pointing their browser to the
Duddy, John wrote:
We'd like to be able to associate fixed things (project, Sample, sequencer
used) with user's FASTQ files, and we'd also like to allow users to associate
dynamic, site-specific stuff with the sequencing run. Currently, users track
their runs using a CSV sample sheet, and
Nate, is it just me or all the .png links on that wikipage are
broken/missing ? :-S
On 2011-05-26 10:38, Nate Coraor wrote:
Duddy, John wrote:
We'd like to be able to associate fixed things (project, Sample, sequencer
used) with user's FASTQ files, and we'd also like to allow users to
I've been configuring my local instance of galaxy to use trackster according to
the instructions on
https://bitbucket.org/galaxy/galaxy-central/wiki/Visualization
when I run the script:
python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/
I get files that begin with:
META
On Thu, May 26, 2011 at 10:34 AM, Roman Valls brainst...@nopcode.org wrote:
Nate, is it just me or all the .png links on that wikipage are
broken/missing ? :-S
I've noticed this on other pages, I think some stuff got moved a while back.
They just need the folder name prefixed...
Peter
Roman Valls wrote:
Nate, is it just me or all the .png links on that wikipage are
broken/missing ? :-S
Hi Roman,
We've had occasional problems with the images in the wiki, and I think
sometimes they'll show up, sometimes they won't. We're in the process
of migrating the wiki to our own Moin
I just checked,
Using the User-Register menu works, however we require our users to log in so
when they go to galaxy.jax.orghttp://galaxy.jax.org they are redirected to a
login page if they are not already logged in. That page has the text This
installation of Galaxy has been configured such
Hi Glen,
I've never seen this before, but perhaps your user controller is using an old
version ( I'm just grasping here, because this is pretty obscure behavior ).
Try deleting the following file - make sure it is the .pyc file.
~/lib/galaxy/web/controllers/user.pyc
The user controller
Just removed user.pyc and restarted the server. Did not resolve the problem.
Dave
On 5/26/11 8:09 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Glen,
I've never seen this before, but perhaps your user controller is using an old
version ( I'm just grasping here, because this is pretty
Hi all,
I am using one tool which gives stdout and stderr . it is showing red color
(job failed) in browser.How can i resolve such type of problem.
Regards
shashi shekhar
___
Please keep all replies on the list by using reply all
in your
You need a wrapper to capture the stderr
It would be nice if there were an option to base a tools status on the unix
return value (for well behaved programs)
On May 26, 2011, at 8:36 AM, shashi shekhar meshash...@gmail.com wrote:
Hi all,
I am using one tool which gives stdout and stderr
On Thu, May 26, 2011 at 1:36 PM, shashi shekhar meshash...@gmail.com wrote:
Hi all,
I am using one tool which gives stdout and stderr . it is showing red color
(job failed) in browser.How can i resolve such type of problem.
Regards
shashi shekhar
See issue 325,
Alternatively you can redirect your STDOUT and/or STDERR into a LOG txt file as
additional output to the tool.
I do many times the same since it allows the realtime tracking in the log file
of the process where it is and when it's expected to be finished.
Indeed a wrapper can be used but if you
On Thu, May 26, 2011 at 1:22 PM, Kempenaar, M (med)
m.kempen...@med.umcg.nl wrote:
Hi list,
I've been working on a single Galaxy tool for a while now, and I'm running
into all sorts of difficulties that can probably all be fixed using Cheetah.
However I've been trying several ways of utilizing
PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT
and STDOUT to a logfile. You won't get a red box though when errors occur!
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: donderdag 26 mei 2011
On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex alex.boss...@wur.nl wrote:
PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT
and STDOUT to a logfile. You won’t get a red box though when errors occur!
Right - if you need to detect an error state via the return code,
On May 25, 2011, at 8:18 AM, Nate Coraor wrote:
Shantanu Pavgi wrote:
On May 19, 2011, at 4:05 PM, Shantanu Pavgi wrote:
I have configured custom cluster_files_directory in universe_wsgi.ini file.
The cluster jobs are running fine, however job scripts, stdout and stderr
are being
As discussed in the Workflows and APIs breakaway session, here is the
paper on Workflow patterns:
van der Aalst, ter Hofsted, Kiepuszewski and Barros, Distributed and
Parallel Databases, Volume 14, Number 1, 5-51: Workflow Patterns
PDF available at:
On Thu, May 26, 2011 at 3:45 PM, Johannes Eichner
johannes.eich...@uni-tuebingen.de wrote:
Hi Peter,
I defined an additional metadata element for the column names
analogously to the column_types element in the module
galaxy_basedir/lib/galaxy/tools/datatypes/tabular.py:
MetadataElement(
That's good news. Is this available via the API as well? I didn't see examples
of this anywhere in the code, but I thought it might be available by passing
additional values in the dictionary.
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Thursday, May 26, 2011
Peter,
can't agree more. Its more a workaround to get warnings not turning up red.
Porting it to the log file would mean you have to check the logfile!
Alex
Van: Peter Cock [p.j.a.c...@googlemail.com]
Verzonden: donderdag 26 mei 2011 16:04
Aan: Bossers,
The sample tracking system looks interesting. It looks like this is designed to
have the sequencers modeled in Galaxy, have Galaxy pull the data from the
sequencers, and might assume 1-1 pairing between sequencing run and samples.
I'd like to be able to support pushing files from a central
Hi Peter,
Thanks very much for you answer, this was exactly the problem, I thought I was
dealing with a Python string and the Cheetah error was not as clear as the
Python error that you'd get when calling a function from an unsupported object.
I also joined in with one of the Breakout sessions
I have my data in a data library and have a form template defined so I can
enter the sample information.
So, I import a data file into a history and want to run a tool on it. Can I
pass the values of those form templates to my tool? Sort of line
${input.form_field_id} ?
Thanks!
John Duddy
On 27/05/11 00:04, Peter Cock wrote:
I regard fixing issue 325 as one of the top priorities in Galaxy
Can't agree more with you Peter!
This bug and other tool wrapper related bugs make it harder and more
tedious to contribute tool wrappers. It's a big turn off for me.
Florent
Can anyone comment on my email please?
Florent
On 22/05/11 14:03, Florent Angly wrote:
Let me know if you have any questions about this.
Thanks,
Florent
Original Message
Subject:Request for pulling the updated FASTQ (de-)interlacer tool
Date: Tue, 17 May 2011
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