On 05/08/2013 05:38 PM, Geert Vandeweyer wrote:
self.sa_session.execute('UPDATE job SET runtime = :runtime WHERE id =
:id',{'runtime':runtime,'id':galaxy_job_id})
does anybody have a solution to convert this statement to proper
sqlalchemy syntax, for use in the check_watched_items function
On Tue, May 14, 2013 at 3:32 AM, Ira Cooke iraco...@gmail.com wrote:
Hi All,
My guess is that one of the most common ways in which tools will fail tests
on the build-bot is when a dependency fails to install properly. I think
this is what is happening to my tool xtandem
Hi Peter,
Yes that's most likely part of it ... thanks for the link to that thread. I
think I am suffering from the same issue.
... but I'm also assuming when my test results come back I'll still need to
figure out where my repository dependencies failed. Last test result I saw it
looked
On Tue, May 14, 2013 at 10:39 AM, Ira Cooke iraco...@gmail.com wrote:
Hi Peter,
Yes that's most likely part of it ... thanks for the link to that thread.
I think I am suffering from the same issue.
... but I'm also assuming when my test results come back I'll still
need to figure out where
We're fairly close to having a new container in the Tool test results
container. The new container will be something like Installation errors and
for each tool it will list the tool dependencies that have installation errors.
Any installation errors will result in the tool not being tested.
On May 14, 2013, at 6:28 AM, Peter Cock wrote:
Dear all,
Something seems to have happened to the lists.bx.psu.edu
server recently - which is unfortunate as I've made a habit
of using this for linking to past email threads via the nice
mailman archive listing which was here:
Hi John,
A few of us in the lab here at Penn State actually discussed automatic creation
of virtualenvs for dependency installations a couple weeks ago. This was in
the context of Bjoern's request for supporting compile-time dependencies. I
think it's a great idea, but there's a limitation
We'd like to trim the the galaxyIndicies/genome directory to human and
blastdb. As we may have several CM instances, we would like to share this
filesystem across all instances.
I would like to simply copy these data to a new volume and mount this
filesystem with all our CM instances. Do I just
Hello Björn,
I've analyzed this and discovered some very important points to make sure
everyone understands, so I hope my information below is very clear. Please
don't hesitate to ask any questions for clarification. The items fall into 2
categories.
First item:
The first item for
On the other hand, if a workflow is imported from a file on disk or from a
URL, tool level annotations are available while workflow level annotations
are not.
This has been fixed in this changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/8882e45504a3/
Thanks for reporting this
On May 14, 2013, at 10:58 AM, John Chilton wrote:
Hey Nate,
On Tue, May 14, 2013 at 8:40 AM, Nate Coraor n...@bx.psu.edu wrote:
Hi John,
A few of us in the lab here at Penn State actually discussed automatic
creation of virtualenvs for dependency installations a couple weeks ago.
Hello all,
Just a reminder that this is happening tomorrow, Wednesday, May 15. If you
haven't taken a look at the Pathogen Portal Galaxy Server (*RNA-Rocket*,
http://rnaseq.pathogenportal.org/) yet, please do.
If you will be on the call, please connect a few minutes early, as it will
take that
Greg created the following card, and I'm working on a few changes to your
commit:
https://trello.com/card/toolshed-consider-enhancing-tool-dependency-definition-framework-per-john-chilton-s-pull-request/506338ce32ae458f6d15e4b3/848
Thanks,
--nate
On May 14, 2013, at 1:45 PM, Nate Coraor wrote:
Awesome, thanks! What about workflows imported from tool shed
repositories? For example, I have two annotated workflows in this
repository: http://testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test.
When I install them from the repository to my local galaxy-central
instance
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