Hi Aneisha,
When you say you cannot alter config/galaxy.ini, what do you mean? You
should be able to create (if not there) and edit this file in your regular
terminal on that machine.
Does a different user own the file, perhaps a 'galaxy' one? If so, you
could change to that user and then edit.
Hi, I work at the It service desk at the GRU Health and Science campus Ed
Commons GB building and I have a customer trying to get admin access for the
local installation of galaxy. We tried to follow the online instructions "In
order to control your new Galaxy through the UI (installing tools, m
Hmm.
That may need a tweak - using GALAXY_TEST_NO_CLEANUP
is not the default, so this could easily be a regression.
Peter
On Fri, Jun 12, 2015 at 6:09 PM, Ryan G wrote:
> I tried that and the directories don't get removed however the job files
> still get deleted.
>
> On Fri, Jun 12, 2015 at 12
done
On Fri, Jun 12, 2015 at 11:33 AM, Nicola Soranzo
wrote:
> Hi Ryan,
> please open a pull request at
> https://github.com/galaxyproject/tools-devteam
>
> The file is in tools/picard/ directory.
>
> Thanks,
> Nicola
>
> Il 12.06.2015 17:23 Ryan G ha scritto:
>
> The functional test for this
I tried that and the directories don't get removed however the job files
still get deleted.
On Fri, Jun 12, 2015 at 12:03 PM, Peter Cock
wrote:
> Hi Ryan,
>
> Something very handy for tool developers running functional tests
> is if the environment variable GALAXY_TEST_NO_CLEANUP
> is set, run_t
Thanks John,
that's quite the detailed response.
I agree with your reasoning, and I can see the progress in planemo -- the
shed_test
command is great and I'm using it to see why some of my tool tests fail.
In this particular case there is nothing wrong with the framework though,
as the planemo tes
Hi Ryan,
Something very handy for tool developers running functional tests
is if the environment variable GALAXY_TEST_NO_CLEANUP
is set, run_tests.sh shouldn't remove the test output.
This is great when debugging why a test is failing.
Peter
On Fri, Jun 12, 2015 at 4:29 PM, Ryan G wrote:
> I'
On Fri, Jun 12, 2015 at 4:37 PM, John Chilton wrote:
> tl;dr - The devteam is planning to remove the display of those test
> results from the tool shed UI and replace them with something better
> hopefully by the end of 2015.
>
>
>
> This may make people unhappy - it certainly doesn't make me hap
tl;dr - The devteam is planning to remove the display of those test
results from the tool shed UI and replace them with something better
hopefully by the end of 2015.
Full Details:
As Peter has documented very well over the last year, there are large
number of problems with the install and test f
Hi Ryan,
please open a pull request at
https://github.com/galaxyproject/tools-devteam
The file is in
tools/picard/ directory.
Thanks,
Nicola
Il 12.06.2015 17:23 Ryan G ha
scritto:
> The functional test for this tool fails. Looking at the XML
wrapper, it looks like $comments is invalidit
I'd like to recommend a change. If jobs fail to run during functional
tests, I'd like to keep the failed job files around to be examined. I
added the following to do so:
+++ scripts/functional_tests.py
@@ -372,6 +372,7 @@ def main():
user_library_import_dir=user_library_i
The functional test for this tool fails. Looking at the XML wrapper, it
looks like $comments is invalidit doesn't exist anywhere else in the
xml file. I know that comments can be specified multiple times however
there is no way to get the comments fields to appear multiple times in the
UI as
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo
wrote:
> Hi Ryan,
> there is no know fix for this, apart from moving to PostgreSQL.
>
> Cheers,
> Nicola
>
> Il 12.06.2015 16:43 Ryan G ha scritto:
>
> Hi all - I'm running functional tests on a set of tools using
The virtual environment still gave me the same Fetch failed error. Any
other options to try?
Thanks,
Medini
On Jun 11, 2015 2:02 PM, "Nicola Soranzo" wrote:
> Hi,
> I'd suggest you to try to run Galaxy in a virtualenv:
>
> $ cd galaxy/
> $ virtualenv .venv
> $ ./run.sh
>
> Cheers,
> Nicola
>
>
Hi Ryan,
there is no know fix for this, apart from moving to
PostgreSQL.
Cheers,
Nicola
Il 12.06.2015 16:43 Ryan G ha scritto:
>
Hi all - I'm running functional tests on a set of tools using
'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run
the tool tests individually,
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh
-sid ...'. A few of the tests fail. When I go back and run the tool tests
individually, they succeed. So I looked into why they fail when running
them in batch, and it turns out to be a database lock. I'm using the
defa
Hello Peter,
I didn't read it in the docs -- I was just assuming that the instance that
runs
the functional tests would have all the dependencies installed, which
appears not to be the case.
Best,
Marius
On 12 June 2015 at 10:41, Peter Cock wrote:
> On Thu, Jun 11, 2015 at 2:43 PM, Marius van
On Thu, Jun 11, 2015 at 2:43 PM, Marius van den Beek
wrote:
> Hi list,
>
> I’ve been trying to write functional tests for a tool that produces BAM
> files as output. The tests run fine when using planemo locally,
> but not on the testtoolshed or on machines that do not have samtools
> installed.
>
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