Hi all,
can anyone confirm that the parallelism features is not working in
galaxy-central? Parallelism is among others used by the blast+ wrappers.
The only error message I get is:
galaxy.jobs DEBUG 2013-03-17 16:08:27,729 (64174) Working directory for
job
is: /media/data/web/galaxy-central/data
On Sun, Mar 17, 2013 at 3:13 PM, Björn Grüning wrote:
> Hi all,
>
> can anyone confirm that the parallelism features is not working in
> galaxy-central? Parallelism is among others used by the blast+ wrappers.
>
> The only error message I get is:
>
> galaxy.jobs DEBUG 2013-03-17 16:08:27,729 (64174
Am Sonntag, den 17.03.2013, 15:26 + schrieb Peter Cock:
> On Sun, Mar 17, 2013 at 3:13 PM, Björn Grüning wrote:
> > Hi all,
> >
> > can anyone confirm that the parallelism features is not working in
> > galaxy-central? Parallelism is among others used by the blast+ wrappers.
> >
> > The only er
On Sun, Mar 17, 2013 at 3:40 PM, Björn Grüning
wrote:
> Am Sonntag, den 17.03.2013, 15:26 + schrieb Peter Cock:
>> On Sun, Mar 17, 2013 at 3:13 PM, Björn Grüning wrote:
>> > Hi all,
>> >
>> > can anyone confirm that the parallelism features is not working in
>> > galaxy-central? Parallelism is
I believe the following changeset fixes this problem.
https://bitbucket.org/jmchilton/galaxy-central-lwr/commits/3b6c209d2d078bad2fa9957fe989345d3d2533ae
I have incorporated the fix into pull request 138 that has other job
runner fixes and enhancements.
-John
P.S.
Peter's point about the taske
Hi John,
works great, thanks for your effort!
> I believe the following changeset fixes this problem.
>
> https://bitbucket.org/jmchilton/galaxy-central-lwr/commits/3b6c209d2d078bad2fa9957fe989345d3d2533ae
>
> I have incorporated the fix into pull request 138 that has other job
> runner fixes a
A new next-stable branch on Galaxy central is currently scheduled for tomorrow
( 3/18/13 ) in preparation for the next Galaxy dist release currently scheduled
for 4/1/13.. This means that the main tool shed will be updated tomorrow to
this next-stable branch.
This branch includes a new tool
Repositories that contain only a tool dependency definition file are a special
kind of repository. The tool dependency is considered an orphan tool
dependency because it is not associated with any tools in the same repository.
This orphan designation is not so important in the tool shed itself
> On Mar 17, 2013, at 2:25 PM, Björn Grüning wrote:
>>
>> Maybe its possible to run a few selected toolshed tools in an automatic
>> test suite before each release or after such large changes. We have
>> really complex tools in the toolshed that uses mainly all features
>> available.
>>
>> Have a n
Oops sorry, meant to keep the list cc'd - resending.
On 18 March 2013 16:18, Clare Sloggett wrote:
> Hi Rob,
>
> Were you using a very old version of the library and examples or was it
> quite recent? In any case, try grabbing the script from
> https://github.com/afgane/bioblend/tree/master/docs
On Fri, Mar 15, 2013 at 9:58 AM, Peter Cock wrote:
> On Fri, Mar 15, 2013 at 2:51 PM, John Chilton wrote:
>> Hey Peter,
>>
>> I wonder if it is better to ask the user what type they would like to
>> select and then have the input param inside the conditional.
>
> That is doable now, but I'm not s
Dear Galaxy Community
I frequently use pileup files in galaxy.
The sequence read column contains characters like .,AaCcTtGgNn$* etc.
I would like to be able to add a column to my tables that represents the number
of instances of a given character in the read column.
I can do this in excel with th
Dear Sir or Madam,
I hope this reaches you well. I am a graduate student at Seton Hall University
and it has been a wonderful experience using Galaxy Project's main server
(https://main.g2.bx.psu.edu/) for the past few months. Unfortunately, I am
experiencing trouble since the update to the ser
Hi all,
This is a using-the-API question; not sure if it belongs in galaxy-dev or
galaxy-user !
There seem to be two ways to retrieve metadata for a dataset, one in the
Histories API and one in the Datasets API. They return different
information.
So for instance if I call
http://galaxy-vic.genom
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