permissions of 644.
I don't see any reason why I shouldn't be able to view or download this file
through galaxy.
Any ideas?
Thanks,
Dave
---
Dave Walton
Manager Scientific Computing
The Jackson Laboratory
Bar Harbor, Maine
dave.wal...@jax.org
The information in this email, including attachments, may
JAX would be interested in this.
Dave
From: Ryan Golhar
ngsbioinformat...@gmail.commailto:ngsbioinformat...@gmail.com
Date: Friday, April 27, 2012 3:14 PM
To: Ann Black-Ziegelbein annbl...@eng.uiowa.edumailto:annbl...@eng.uiowa.edu
Cc:
Minor correction. It wasn't commented out...
# Force everyone to log in (disable anonymous access).
require_login = True
But yes, changing to
Require_login = False
Fixed the problem.
Thanks Iry.
Dave
On 9/1/11 8:42 AM, Iry Witham iry.wit...@jax.org wrote:
Hi Nate,
We have found
routinely use for metadata needed at
some final amalgamation step, such as experimental condition) is hard
to find in all the cruft.
On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton dave.wal...@jax.org wrote:
This is similar to something we've done for workflows in our instance of
Galaxy
I'm building a tool that needs the display name of a file inside the
output of the tool.
To clarify, I have a tool that merges gene expression result from cufflinks
for many samples. It generates a matrix tab-delimited file that provides
the results with genes or transcript down one axis and
than 1?
Is the behavior occurring for all of your users or just a few? Does it occur
with different browsers, or is it related to a certain browser brand?
What version of Galaxy are your running?
Thanks Dave,
Greg Von Kuster
On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg,
We've tried
than 1?
Is the behavior occurring for all of your users or just a few? Does it occur
with different browsers, or is it related to a certain browser brand?
What version of Galaxy are your running?
Thanks Dave,
Greg Von Kuster
On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg
We upgraded our Galaxy instance to the current Dist build at the end of last
week. Since then we've had a couple new users attempt to create accounts.
When they go to the create user page (http://galaxy.jax.org/user/create)
they get a 500 Server Error.
The message in the error log is:
/compiled_templates/user assuming you have not changed the setting
for the template cache in your universe_wsgi.ini file. If you have, delete
the files in the user directory where you have them stored.
Greg Von Kuster
On May 24, 2011, at 4:02 PM, Dave Walton wrote:
We upgraded our
I'd like to get a better understanding of the point of the database/build
attribute, and pose the question of when is the appropriate time to have it
set?
In our case at the Jackson Laboratory, the most common build is NCBI37/MM9.
However, the feeling of many folks here, is that this should not
An alternative might be to have something like GenePattern has. It's not as
seamless for the person who wants the wrapper as what's been suggested here,
but it's easier than creating a lengthy XML file.
GenePattern has an HTML Form interface for entering all the components of
your tool,
Could someone who has successfully gotten the IGV tool to work using NGINX as
your proxy, tell me if there was anything specific they needed to do with their
NGINX or galaxy config to get it working?
Thanks,
Dave
On 4/27/11 9:07 PM, Dave Walton dave.wal...@jax.org wrote:
I’m getting
I’m getting this same error and I’m running nginx as a proxy server. Is there
a specfic parameter we should be aware of to allow partial gets? I don’t see
anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave
On 4/27/11 12:33 PM, Daniel Blankenberg d...@bx.psu.edu
I'm getting inconsistent behavior when I run a workflow.
I have one workflow,that when I run it, the green box indicating my workflow
has been submitted shows up in the middle panel with Tools to the left,
histories to the right, and menu above.
For another workflow, I submit it successfully,
haven't seen any
errors like this yet.
Also, what's different about the two workflows (history destinations,
multiple-inputs, rename actions, etc.)?
-Dannon
On 04/19/2011 03:01 PM, Dave Walton wrote:
I'm getting inconsistent behavior when I run a workflow.
I have one workflow,that when I
parameters being
the same.
Where are the docs and information for the Galaxy API? Wondering if I could
program this exact functionality in the script that the tool would execute.
thanks,
Leandro
On Fri, Apr 15, 2011 at 4:28 PM, Dave Walton dave.wal...@jax.org wrote:
I've essentially asked the same
I've essentially asked the same question of the list in the past and gotten no
real response.
I have the same interest, but from a workflow perspective.
* A module that allows me to select multiple datafiles (say fastq files)
* Then pass each data file to a separate instance of a workflow that
I'm working on a module that involves calling a workflow multiple times over a
set of data.
The workflow has a variable that I use for renaming output files.
I see, using the workflow_execute.py example how to pass in file names, but I
don't see how to pass in a value for this variable.
When
This is very close to our config, except -
We run all of this on a 4 core Virtual Machine running SUSE Linux Enterprise
Server 11 (x86_64) with 16 GB of memory.
Instead of SGE our HPC cluster uses Torque/Moab for scheduling.
Also, we've set up a separate IO Node for upload of data files from the
/11 11:23 AM, Dave Walton dave.wal...@jax.org wrote:
I'm curious if there is a way to create a workflow as follows (or if anyone
else thinks this is a good idea, or for that matter has a good suggestion of
another solution):
1) User selects N groomed fastq files and puts them in a history
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