Hello, all
First , I apologise if am posting in wrong forum!,
I would like to learn how to conduct research on population genomic and am
looking for recommendations for good material such as tutorials,books and
course outline.
thank you
huu
Peter,
Thanks for reporting this issue, it looks like there might be a bug in
tool_list.py, which I will be looking into. In the meantime, you should
still be able to run functional tests for your tool by executing
sh run_functional_tests.sh -id
Where is the ID you have defined in the tool
David,
While I look into the cause of this error, could you tell me which
revision of Galaxy you're running?
--Dave B.
On 4/11/13 12:51:03.000, David Bonsall wrote:
Dear Galaxy team,
I'm trying to install NCBI + tools on a local instance of galaxy (rep:
8.1546099212f), but I get the foll
Peter,
The automated testing framework is also running against the test tool
shed. Could you send me a link to the repository that is behaving oddly?
--Dave B.
On 4/12/13 06:42:04.000, Peter Cock wrote:
Hi all,
I'd like to be able to experiment with the new automated testing
recently add
Hi,
Our galaxy instance runs jobs in a SGE cluster using 2 job-handlers. The
SGE cluster uses a Job Submission Verifier (JSV) that rejects any job
submission that specify core
binding strategies.
When Galaxy starts, the first jobs we submit works perfectly:
First job submission:
galaxy.jobs
On Mon, Apr 15, 2013 at 2:20 PM, Dave Bouvier wrote:
> Peter,
>
> The automated testing framework is also running against the test tool shed.
> Could you send me a link to the repository that is behaving oddly?
>
e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
On the main tool s
On Mon, Apr 15, 2013 at 2:15 PM, Dave Bouvier wrote:
> Peter,
>
> Thanks for reporting this issue, it looks like there might be a bug in
> tool_list.py, which I will be looking into. In the meantime, you should
> still be able to run functional tests for your tool by executing
>
> sh run_functiona
Peter,
Thanks for the contribution, I've verified that it works, and it has
been committed in 9395:388e86c30bad.
--Dave B.
On 4/15/13 09:59:46.000, Peter Cock wrote:
On Mon, Apr 15, 2013 at 2:15 PM, Dave Bouvier wrote:
Peter,
Thanks for reporting this issue, it looks like there might b
On Mon, Apr 15, 2013 at 3:12 PM, Dave Bouvier wrote:
> Peter,
>
> Thanks for the contribution, I've verified that it works, and it has been
> committed in 9395:388e86c30bad.
>
>--Dave B.
Great, thank you :)
Peter
___
Please keep all rep
Peter,
I'm unable to duplicate that behavior, the "View tool functional test
results" option shows up on the test tool shed both when I'm logged in
and logged out. My suggestion would be to clear your browser's cookies
and cache, and see if that makes a difference.
--Dave B.
On 4/15/13 0
On Mon, Apr 15, 2013 at 3:56 PM, Dave Bouvier wrote:
> Peter,
>
> I'm unable to duplicate that behavior, the "View tool functional test
> results" option shows up on the test tool shed both when I'm logged in and
> logged out. My suggestion would be to clear your browser's cookies and
> cache, and
That does sound like a useful option, I'll be discussing that and other
enhancements to the automated testing system with Greg in the near future.
In this specific case, it looks like functional tests were set to not be
executed, because two of the tools in the repository were missing
function
On Thu, Apr 4, 2013 at 9:47 PM, Peter Cock wrote:
> Hi all,
>
> I've been looking at the new functional test results now being
> shown on the tool shed, and found a bug/glitch:
>
> 1. Goto http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> 2. Click on top right menu "Repository Actions
On Mon, Apr 15, 2013 at 4:14 PM, Dave Bouvier wrote:
> That does sound like a useful option, I'll be discussing that and other
> enhancements to the automated testing system with Greg in the near future.
>
> In this specific case, it looks like functional tests were set to not be
> executed, becau
Hi,
is there a general rule to handle dependencies inside of
tool_dependencies.xml?
Lets assume I write a matplotlib orphan tool_dependencies.xml file.
matplotlib depends on numpy. Numpy has already a orphan definition.
Is there a way to include numpy as dependency inside the
matplotlib-definit
Hi Greg,
> If numpy is not required for compiling matplotlib components (i.e.,
> matplotlib components just use numpy after installation),
> then you should be able to make this work using a complex repository
> dependency for numpy in your tool_dependencies.xml definition for matplotlib.
>
Hi,
After a crash recovery and a second trial I must admit that I cannot
upgrade our galaxy instance.
I need some help...
the facts:
initial instance:
$ hg head
changeset: 8796:961ae35ba612
branch: stable
tag: tip
parent: 8794:1c7174911392
user:Nate Coraor
date:
This looks like just a configuration file problem. What is the value
of the various static_ options (like static_dir =) in your
universe_wsgi.ini?
On Mon, Apr 15, 2013 at 7:25 PM, Christophe Antoniewski
wrote:
> webapp = wrap_in_static( webapp, global_conf, **kwargs )
> File "/home/galaxy
Hi Björn,
On Apr 15, 2013, at 6:31 PM, Björn Grüning wrote:
> Hi Greg,
>
>> If numpy is not required for compiling matplotlib components (i.e.,
>> matplotlib components just use numpy after installation),
>> then you should be able to make this work using a complex repository
>> dependency fo
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