On Tue, 3 Apr 2012 15:06:05 -0600
Nate Coraor n...@bx.psu.edu wrote:
If I enable apache_xsendfile, the little eye icon (Display data in
browser) on each dataset stops working. I get the following instead:
The requested URL /datasets/7e93e3cf926fb2b3/display/ was not found on this
Hello,
I am looking for the way to go to include JAVA jar or classes into a
Toolshed tool.
I noticed that JARs are gathered in galaxy-dist/tool-data/shared/jars.
e.g. below:
java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar
What I did, I placed the java class next
Hmm,
I start feeling like I'm only talking to myself here :-)
I finally have a prototyp running.
Currently the mapping galaxy username - cluster username is only done using a dictionary in
dmraa.py and should (and will) be moved to a configuration file.
(Even better would be to put that into
Hello All,
Is there a way to set auto delete some datafiles at the end of workflow run?
I'm asking this because it is sometimes useful to delete some outputs (say
intermediate files, .logs, etc), for example auto delete .sam file after
executing sam-to-bam tool, which would free-up lot of
On Wed, Apr 4, 2012 at 12:30 PM, Praveen Raj Somarajan
pravee...@ocimumbio.com wrote:
Hello All,
Is there a way to set auto delete some datafiles at the end of workflow
run? I'm asking this because it is sometimes useful to delete some outputs
(say intermediate files, .logs, etc), for
exactly, something similar to auto-hide feature. This would be a nice option
to have, as the intermediate files consume huge amount of memory, especially in
case of NGS analysis.
- Raj
-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: Wednesday, April 04,
Hi,
I've been working off of a local instance of Galaxy (6799:40f1816d6857) to
develop tools and I'm running into some issues which I'm not sure how to
resolve idiomatically.
First, some of the tools I'm trying to write Galaxy wrappers for take a
directory as input. The directory contains
Dear Galaxy users,
I have installed a local Galaxy instance in my university's server. Recently I
encountered a problem whenever I try to load Galaxy into my browser. When I
press the link it starts loading but it never ends resulting with a timeout
error. Has anyone encountered this problem
On Apr 4, 2012, at 11:11 AM, Langhorst, Brad wrote:
I'm no authority... but given that nobody else has replied yet I'll give my
opinion.
I think I would approach the directory problem with a wrapper script that
takes arguments for each of the components needed by the tool.
The script
On Apr 4, 2012, at 1:48 PM, Aaron Gallagher wrote:
On Apr 4, 2012, at 8:11 AM, Langhorst, Brad wrote:
I think I would approach the directory problem with a wrapper script that
takes arguments for each of the components needed by the tool.
The script could lay out the various files as
On Apr 4, 2012, at 2:44 PM, Aaron Gallagher wrote:
On Apr 4, 2012, at 11:35 AM, Langhorst, Brad wrote:
This is somewhat akin to the reference area galaxy uses to store reference
sequences (and their various indices, formats, annotations etc).
It might be possible to modify galaxy's
Dear all,
I followed the instructions under the link
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy to set up a Apache
proxy to Galaxy.
I have done with the section of basic configuration and it works very well.
However when I move to the next section: external user authentication, I
found
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