Hi Paul,
the EMBOSS Tools are located in the http://toolshed.g2.bx.psu.edu/. You
need to install them from there.
http://wiki.g2.bx.psu.edu/Tool%
20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
Hope that helps!
Bjoern
Hi,
I'm trying to enable
Hello,
I apologize for this probably very simple application.
We have installed our own Galaxy server and started using in-house the
NGS modules. However, during the mapping procedure using either BWA for
illumina or BFAST tools, no reference genome index is available.
To solve the problem, we
Dear list,
I am running galaxy-dist on Amazon EC2 through Cloudman, and am using
the enable_tasked_jobs to run jobs in parallel. Yes, I know it's not
recommended in production. My jobs usually get split in 72 parts, and
sometimes (but not always, maybe in 30-50% of cases), errors are
Hi paul,
We'll need enough information from your paster log to determine the problem.
If your server threw an exception, you may also have a stack trace in your
browser window and we'll need that infomration as well.
Thanks,
Greg Von Kuster
On Sep 13, 2012, at 10:38 PM, Paul Tanger wrote:
Hi all,
I have a problem with one of applications of galaxy-cistrome : when I run
the application Heatmap, it didn't work and the log says me : need
bx-python
It's very clear. but on another pc with same installation, Heatmap run and
furthermore bx-python is installed with your procedure : in
*Not sure if this is what you need, but here is the info from the error
page. I obscured part of the IP address.*
URL:
http://129.XX.XX.XX:/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=f2db41e1fa331b3e
File
ok, I forgot to set a directory for the tool dependencies in the new
install, and once I did that it worked!
On Fri, Sep 14, 2012 at 11:58 AM, Paul Tanger paul.tan...@colostate.eduwrote:
*Not sure if this is what you need, but here is the info from the error
page. I obscured part of the IP
Paul,
Glad to hear things are working. The next install should go more easily now
that you've done the first one, which is always the hardest.
Let us know if you bump into any issues in the future.
Greg Von Kuster
On Sep 14, 2012, at 2:11 PM, Paul Tanger wrote:
ok, I forgot to set a
I've run into one bug and a one other smaller issue with the Tophat2
wrapper.
The bug manifests itself when running the tool with use Defaults
selected results in the following error:
cp: cannot stat
`/data/galaxy-dev/galaxy-dev/database/job_working_directory/000/281/tophat_out/fusions.out':
We're seeing an odd issue that seems to be related to Trackster's caching of
track information, mainly that memory in the web server processes increases.
It appears that tracks are being cached in memory per web process.
If I create a new visualization (and monitor our web processed via top)
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