On Wed, Sep 10, 2014 at 7:55 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi Peter,
This was due to a bug I introduced last week, which I've just fixed in
d1f6d05. Sorry for the trouble.
--nate
Thanks - I'll check back in a day or two once the tests have
run again.
Peter
Hi Melissa,
a few remarks to your wrappers, hopefully it will fix a few issues.
* If you put your python files and your java files next to your wrapper
you do not need to install them. I think you can remove the
tool_dependency file and it should work.
* if you stick to this approach you
Christophe,
Unfortunately, exporting a capsule without a proxy in front of the tool
shed will fail to find dependencies if the dependencies were defined
with the proxy in place. One solution would be to re-upload the
dependency definitions without using the proxy, leaving the
Hi Sebastian,
As for Galaxy Main (usegalaxy.org), our process is automated with Ansible,
the playbook for which can be found here:
https://github.com/galaxyproject/usegalaxy-playbook
A bit of documentation on what you should look for (new versions of
universe_wsgi.ini.sample,
Hi Nate,
Thank you very much for enlightening me - I tried to get an impression on
Ansible playbooks for the last two minutes and I am really exited about
it. Principle and syntax are close to what we are doing in plain BASH plus
config files, but the respective scripts are for sure more complex,
Hi,
I wrote a script which need to retrieve a list of all users on our
production instance.
It seems that we have too many users (325) :P
bioblend.galaxy.client.ConnectionError:
HTTPConnectionPool(host='galaxy.sb-roscoff.fr', port=8080): Max retries
exceeded with url:
Derek:
Just to let you know that I just wrapped BAMTools for Galaxy:
GitHub - https://github.com/nekrut/bamtools
GalaxyToolShed - https://toolshed.g2.bx.psu.edu/view/anton/bamtools
Galaxt Test Server - https://test.galaxyproject.org (look for BAMTools on
the left pane).
We will roll them out on
Dear Galaxy team,
i tried to run the varscan somatic tool from fcaramia on two pileup files
but i got the following error:
Unknown Input: COMMAND::java -jar
/home/karin/galaxy/dependency_dir/VarScan/2.3.5/fcaramia/varscan/51969e284317/jars/VarScan.v2.3.5.jar
somatic
The command was the
Dave,
Thank you very much, it worked indeed.
The gz export does not work yet, but this is apparently now due to a
problem with mercurial (An error occurred while processing your request: -
Archive type not allowed: gz).
Anyway, this is not a main issue and we are going to be able to focus on
the
Just a hunch, do you guys think pysam is the cause of these issues?
From: ashis...@hotmail.com
To: dannon.ba...@gmail.com
CC: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Installing Galaxy on Freebsd 10.0
Date: Wed, 10 Sep 2014 19:21:33 -0500
Hi Dannon,
Thanks for the reply.
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