On Fri, Nov 1, 2013 at 2:13 PM, John Chilton wrote:
Hmmm... I have been thinking a lot about this. I imagine at some point
the nightly tool shed tests will include options for testing install
procedures - I think Peter wants this but is too afraid to come out an
ask for it :).
Ha ha. Am I
I know this has been needed for quite some time. I't's definitely on our near
radar. I'm thinking that testing repositories of type
tool_dependency_definition would cover this request since any repositories that
have bot tools and a tool_dependencies.xml file are already tested. Will this
On Sat, Nov 2, 2013 at 1:38 PM, Greg Von Kuster g...@bx.psu.edu wrote:
I know this has been needed for quite some time. I't's definitely
on our near radar.
Excellent - can we move that Trello card to In Planning? ;)
I'm thinking that testing repositories of type
tool_dependency_definition
On Thu, Oct 31, 2013 at 7:41 AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi,
Hi John Greg,
yes I can confirm that. Thanks for reproducing.
Btw. should I set up one test repository for every feature (lets say for
ruby and R) that will stay like it is and function as test
Hi Greg,
seems to work! Thanks!
Bjoern
I believe this is fixed in 11184:d2b9f616e66c - at least everyting worked for
me. However, committing to next-stable was a bit tweaky although I think all
is ok. Please let me know if you see any problems.
Thanks!
Greg Von kuster
On Oct 30,
Hi,
Hi John Greg,
yes I can confirm that. Thanks for reproducing.
Btw. should I set up one test repository for every feature (lets say for
ruby and R) that will stay like it is and function as test environment.
Or should be write some unit tests for it?
Well if you are going to
Hello Bjoern,
The changeset to which your link refers is the change that allows anyone that
has write permission on a repository to reset all metadata on that repository
from the Repository Actions pop-up menu on the View repository page.
Previous to this change, this feature was restricted
Hi Greg,
sorry for the confusion. You answered to Saskia
This was indeed a bug (not abut which was a spell checker spelling
error) which has been resolved in 6:83bed9c7dbbc. This fix has
If I search for that number I only find your fix for the repository
action view. But I'm searching
I can verify augustus doesn't work correctly any longer, but I do not
get the same error. The package installs properly but set_environment
doesn't get handled.
As far as I can tell this changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877
Hello Bjoern,
Can you confirm that you have the following status for your tool dependencies
when you attempt to install your augustus repository from the main tool shed?
I haven't tracked down the reason that the AUGUSTUS_SCRIPT_PATH dependency is
in the Never installed state. Is this
Thanks John,
I just sent my message as yours arrived - this will help me more quickly
resolve the issue. I'll have a fix soon.
Greg Von Kuster
On Oct 30, 2013, at 4:09 PM, John Chilton chil...@msi.umn.edu wrote:
I can verify augustus doesn't work correctly any longer, but I do not
get the
Hi John Greg,
yes I can confirm that. Thanks for reproducing.
Btw. should I set up one test repository for every feature (lets say for
ruby and R) that will stay like it is and function as test environment.
Or should be write some unit tests for it?
Thanks,
Bjoern
Thanks John,
I just sent
On Wed, Oct 30, 2013 at 3:58 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi John Greg,
yes I can confirm that. Thanks for reproducing.
Btw. should I set up one test repository for every feature (lets say for
ruby and R) that will stay like it is and function as test
I believe this is fixed in 11184:d2b9f616e66c - at least everyting worked for
me. However, committing to next-stable was a bit tweaky although I think all
is ok. Please let me know if you see any problems.
Thanks!
Greg Von kuster
On Oct 30, 2013, at 4:09 PM, John Chilton chil...@msi.umn.edu
Hi Greg,
do you mean that patch?
https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc
I can reproduce that error and it is not fixed with latest
galaxy-central, or did you only applied it to next-stable?
You can test with my augustus repository if you like.
Hello Saskia,
This was indeed a bug (not abut which was a spell checker spelling error)
which has been resolved in 6:83bed9c7dbbc. This fix has been committed to
the next-stable branch and is currently running on both the test and main
Galaxy tool sheds. Thanks for reporting this issue.
I updated my Galaxies to the latest version today, and when I try to install a
toolshed repository which defines an environment variable via the
set_environment tags in the tool_dependencies.xml file, I get an error (see
below).
tool_dependencies.xml:
?xml version=1.0?
tool_dependency
Hello Saskia,
I haven't had a chance to look into this problem, but it's next on my list. If
both of the definitions you list worked in the past, then I believe they should
still work. It's possible tha t abut was introduced somewhere, and if so, I'll
track it down and get it corrected. I
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