Galaxy type: local
I'm trying to get IGV to download files served from the galaxy instance
through display_application.
When IGV makes a request for the BAM file, it is re-routed to root like so:
wget
Sorry, the subject should read mistakenly routed to root. The question
still stands.
-r
On Fri, Jun 22, 2012 at 2:10 PM, Rob Syme rob.s...@gmail.com wrote:
Galaxy type: local
I'm trying to get IGV to download files served from the galaxy instance
through display_application.
When IGV makes
The problem seems to be in the lack of authentication by the request sent
by IGV. The galaxy instance is set to require a username and password with
require_login = True in universe_wsgi.ini, which means that when IGV
attempts to download the BAM file at
On Jun 21, 2012, at 4:50 PM, Dorset, Daniel C wrote:
I have galaxy running on my institution’s cluster computing service, which
uses PBS. It’s in a balanced configuration.
Jobs going to the cluster submit without any problem at all. However, any job
that I have specified to run locally
While I have not yet added IGV for display, I would like to and I would also
like to add tablet so I'm interested in how this plays out.
Hopefully someone more knowledgable will chime in.
Meanwhile, I'll try to help. I think that the 302 redirect indicates that
REMOTE_USER is not being set or
On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:
I have recently performed a fresh installation of Galaxy utilizing the latest
distribution and am getting a sizable number of errors when attempting to
start the server. The issue started when I performed a merge so I decided to
do the clean
Good catch, thanks Nate! I have plenty of tool_runners defined, but no
tool_handlers. Do I have to specifically assign tool handlers in order for them
to be used in job deployment?
Thanks!
Dan
Hi Daniel,
This parameter should be 'job_handlers'
Are there any entries in your
On Jun 22, 2012, at 12:26 PM, Dorset, Daniel C wrote:
Good catch, thanks Nate! I have plenty of tool_runners defined, but no
tool_handlers. Do I have to specifically assign tool handlers in order for
them to be used in job deployment?
No, if you don't define any specific handlers in the
Hi Robert,
This section of the tool shed wiki should provide the information you need.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel
Greg Von Kuster
On Jun 21, 2012, at 5:33 PM, Robert Chase wrote:
Hello,
We are trying to perfect some of the details
Hi Rob,
Changeset 7300:f197c4346cc4, which is currently available in galaxy-central,
should allow the external display applications to work when require_login =
True, thanks for reporting this error. Please let us know if you encounter
additional issues.
Thanks for using Galaxy,
Dan
On
Hello Birgit,
I've committed a fix for this is change set 7302:c4f325ba7caa, which is
available in the Galaxy central repository, and is running on both Galaxy tool
sheds. I've made sure that your cg_cgatools_linux repository is now
functional.
Thanks very much for finding this additional
Hello,
I am having an issue with getting the FastQC tool to work with Galaxy on
our server. I downloaded the FastQC files (version 0.8.0) and changed the
directory that the wrapper script looks for the 'fastqc' executable in, but
when we run a job with it we have been getting the following
Do you run an X11 virtual frame buffer - eg Xvfb?
Otherwise AFAIK R graphics and Java will complain on headless nodes.
On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com wrote:
Hello,
I am having an issue with getting the FastQC tool to work with Galaxy on our
server. I
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