Hi,
Thanks for your answer.
I've no failed job in my history.
I've checked the workflow and it is the same as before update.
But your answer highlight another point ! The tool I use in my final
step has been modified after update of galaxy and not tested alone.
When I've tested this tool alone,
Hi John,
As I specified it in the edit of my first message, I have this error
only if I run groomer with a command line in another xml file
surrounding by other command. When I run groomer alone with the
original xml, it works fine, so no problem with the PYTHONPATH.
But when I use this :
Hi all,
I'm trying to package my tool wrapper to release it in the ToolShed. I
need to download the associated binary file and change the permissions.
I wrote a tool_dependency xml file with a downlod_binary and chmod actions.
My tool_dependency_dir is well defined in my universe file. The
I've found it:
I've modified it in the file universe_wgsi.ini and now I can delete user by the
admin tool panel.
The problem is: when I delete the account and purge it why it still remain in
the list ? is it possible to delete it completely ??
From: leonardsqual...@hotmail.com
To:
That error sounds like it's trying to merge the current working directory with
the path supplied in the CHMOD tag.
current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) -- join
work_dir with dir
You have 2 possibilities to try:
1. Eliminate the $INSTALLDIR from the path in the XML
Hi,
I try to apply functional tests of tools against my instance of Galaxy.
When I launch run_functional_tests.sh with the default behavior on the
local machine for running the tests it works.
But when I try to run tests against an external instance deployed on
http://138.102.22.90:8080 and
Hello Stéphane,
To the best of my knowledge this feature has been broken for several years.
-John
On Mon, Jul 7, 2014 at 8:51 AM, speil...@jouy.inra.fr wrote:
Hi,
I try to apply functional tests of tools against my instance of Galaxy. When
I launch run_functional_tests.sh with the
Opps sorry about that - I sent that last e-mail out before I meant to.
As I was saying - I believe that feature has been broken for years and
there is a Trello card to track progress on and vote for here:
https://trello.com/c/8K86l4Qk.
-John
On Mon, Jul 7, 2014 at 9:00 AM, John Chilton
Ahhh - I get it now. Galaxy only adds itself to the PYTHONPATH if it
can infer it is running a Python script (i.e. the command block starts
with python or a Python interpreter is used).
If you are building a tool for the tool shed - it would be best to
setup a tool dependency on the
Thanks!
Actually it's not for the toolshed, for the moment...
But I'm very intereseted by details to install it into a virtualenv.
Thank you.
Julie
2014-07-07 16:16 GMT+02:00 John Chilton jmchil...@gmail.com:
Ahhh - I get it now. Galaxy only adds itself to the PYTHONPATH if it
can infer it is
If your tool defines a package requirement like:
requirements
requirement type=package version=1.0.0galaxy-sequence-utils/requirement
/requirements
And your tool_dependency_dir setting universe_wsgi.ini is something
like /data/galaxy_deps - then you should be able to create a file
Hello,
I am writing to inquire if there are considerations which would prevent
creation of multiple instances of Galaxy by cloning a reference Galaxy
installation containing a pre-configured set of tools and related assets. Both
the reference and cloned instances would reside in the same
Hi Srinivas,
I'm not sure I entirely understood your questions, its to late for me
today sorry. But maybe you would like to have a look at:
https://github.com/bgruening/docker-recipes
It's basically a docker base image (galaxy) on top you can create
several specialised images can be created
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