Based on the screenshot you are calling the program correctly.
Can you tell me what version of Docker you are running and Galaxy you
are running? There have been a number of fixes in both programs over
the last six months to a year. Docker is known to consume a lot of
space in /var - it probably d
Slight clarification on that -- main toolshed update is a separate process
since it runs #stable, but we're working on getting that updated as well.
On Fri Jan 30 2015 at 12:26:06 PM Dannon Baker
wrote:
> I'm actually working on rolling out much better error capturing for the
> toolshed via sent
I'm actually working on rolling out much better error capturing for the
toolshed via sentry (getsentry.org) and expect to update the test toolshed
again with it shortly. I'd guess the main toolshed won't be too far behind.
On Fri Jan 30 2015 at 12:24:47 PM Peter Cock
wrote:
> Hi Dannon, Nicola,
Hi Dannon, Nicola,
This sounds very promising - I'll rerun the TravisCI job and we can
expect it to work this time :)
https://bitbucket.org/galaxy/galaxy-central/commits/3618b7a91e23096ecf7ce5842c1e16c749251a4d
(half an hour ago!)
When will this reach the Tool Shed and Test Tool Shed? The upload
Yep, the FutureWarning that that commit resolves would have caused the
upload job to end up as an error; I'm betting this is what was causing
Peter's issues too.
On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo
wrote:
> Hi Peter,
> I was also getting "Exception: History in error state" errors w
Hi Peter,
I was also getting "Exception: History in error state"
errors with BioBlend continuous integration testing, but those seem to
be fixed with latest Dannon's commit
3618b7a91e23096ecf7ce5842c1e16c749251a4d .
Nicola
Il 30.01.2015 17:36
Peter Cock ha scritto:
> Retitling thread,
>
> On
Retitling thread,
On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock wrote:
> Thanks Dave,
>
> The good news is yes, the tests are running again on the
> Test Tool Shed (although not the main Tool Shed yet), and
> many of my tools now have successful test results from
> last night.
>
> e.g. My new basic
On Thu, Jan 29, 2015 at 4:43 PM, Joseph Brent Greer
wrote:
> Hi all,
>
>
>
> We have Pulsar working in a synchronous fashion using RESTful services on
> our local network. Now, we’re trying to use Pulsar on a remote (SGE) cluster
> and we will not have the ability to mount a shared file system.
>
Hi Anne,
moving the whole Galaxy installation is a tough job and we do not really
have a good process for it. Your problem is most probably caused by the
inconsistency in the DB. The path to the shed_tool_conf.xml is stored there
and the changes you made to the location of the installation did not
On Fri, Jan 30, 2015 at 9:24 AM, Shrum, Donald C wrote:
> Hi all,
>
>
>
> I’ve configured one of our tools to submit jobs to our condor cluster. I
> can see the job is routed to the condor runner:
>
>
>
> ==> handler4.log <==
>
> galaxy.jobs.handler DEBUG 2015-01-30 09:14:58,092 (508) Dispatching
Bjoern's answer is a good one. Another way we commonly do this is by
preparing a 'base' history published with the datasets the students need to
get started -- something like
https://usegalaxy.org/u/mimi31k/h/chip-seq-example-1-raw-data. Students
then click a single button to import that history
Hi Edgar,
this is indeed possible. Please have a look at Galaxy data libraries:
https://wiki.galaxyproject.org/Admin/DataLibraries/Libraries
Cheers,
Bjoern
Am 30.01.2015 um 15:30 schrieb Fernandez Edgar:
> Good morning Gents,
>
> I hope everyone is well.
>
> I was wondering if it's possible t
Good morning Gents,
I hope everyone is well.
I was wondering if it's possible to share data on Galaxy without all the users
downloading the data to their history.
Let me explain, teachers will be sharing data with their students.
And the students will need to work with that specific data.
Howeve
Hi all,
I've configured one of our tools to submit jobs to our condor cluster. I can
see the job is routed to the condor runner:
==> handler4.log <==
galaxy.jobs.handler DEBUG 2015-01-30 09:14:58,092 (508) Dispatching to condor
runner
galaxy.jobs DEBUG 2015-01-30 09:14:58,204 (508) Persisting
On Fri, Jan 30, 2015 at 2:07 PM, Dannon Baker wrote:
> On Fri Jan 30 2015 at 5:36:29 AM Peter Cock
>>
>> >> https://toolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owner=peterjc&status=all
>> >>
>> >> Internal Server Error
>> >> ...
>> >
>> > Trello issue logged,
>> >
>> > https://trello
On Fri Jan 30 2015 at 5:36:29 AM Peter Cock
>
> >> https://toolshed.g2.bx.psu.edu/repository/get_functional_
> test_rss?owner=peterjc&status=all
> >>
> >> Internal Server Error
> >> ...
> >
> > Trello issue logged,
> > https://trello.com/c/ZOW0NPzb/2378-main-toolshed-rss-feed-
> for-test-results-of
On Thu, Jan 29, 2015 at 12:08 PM, Peter Cock wrote:
> On Tue, Jan 27, 2015 at 1:25 PM, Peter Cock wrote:
>>
>> On Tue, Jan 27, 2015 at 11:32 AM, Peter Cock
>> wrote:
>> > On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier wrote:
>> >> Peter,
>> >>
>> >> After fixing a number of issues, it appears th
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