Dear Galaxy Team,
We would like to benchmark CloudMan with NGS data in Tokyo,
and we are wondering if it is possible to launch it at AWS's Tokyo DC
in order to facilitate large-size data transfer and low-latency response.
However, CloudMan AMI is currently available only at Virginia DC
according
On Mon, Oct 7, 2013 at 8:52 PM, Björn Grüning
wrote:
>>
>> Hi Dave, Bjeorn,
>>
>> Right now NumPy isn't installing at all on the Test Tool Shed.
>>
>> Dave - is is possible that the system was updated and the
>> Fortran compiler removed? e.g.
>>
>> ...
>>
>> Since this seems to be breaking lapack,
Title was: [galaxy-iuc] Platform-specific tool dependency support has
been enhanced.
On Fri, Oct 4, 2013 at 6:08 PM, Dave Bouvier wrote:
> Peter,
>
> Thank you for reporting that error, I've committed a fix in
> 10791:6e063ca1960f.
>
> --Dave B.
Hi Dave,
The new platform specific actions seem
Splitting off from this thread:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-October/016903.html
On Mon, Oct 7, 2013 at 4:24 PM, Dave Bouvier wrote:
> Peter,
>
> The platform detection code is not yet in the stable branch, but is intended
> to be included in the upcoming release. The automat
On Tue, Oct 8, 2013 at 4:48 AM, Ryota Yamanaka <
yaman...@genome.rcast.u-tokyo.ac.jp> wrote:
> 1) Do you plan to clone CloudMan AMI to other regions outside the US
> in the near future?
> 2) Or, is there any way we can build CloudMan in such regions, with or
> without your support?
>
Yes, we do p
On Tue, Oct 8, 2013 at 6:45 AM, Peter Cock wrote:
> The "Test Tool Shed" is (as I understand it) effectively running
> galaxy-central (presumably updated daily or something like that),
> so it tests the latest and greatest Galaxy code-base and all the
> new Tool Shed features like the new enhance
Hi Greg, Jean-Frédéric,
I'm returning to this old thread rather than starting a new one,
since it is nicely aligned with something I wanted to raise.
On Tue, Feb 19, 2013 at 2:23 PM, Greg Von Kuster wrote:
> Hello Jean-Frédéric,
>
> Sorry for the delay in this response. Please see my inline com
On Tue, Oct 8, 2013 at 3:19 PM, Carlos Borroto wrote:
> On Tue, Oct 8, 2013 at 6:45 AM, Peter Cock wrote:
>> The "Test Tool Shed" is (as I understand it) effectively running
>> galaxy-central (presumably updated daily or something like that),
>> so it tests the latest and greatest Galaxy code-bas
Consider the following sequence:
1. Goto http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan
2. The README file explains this is for InterProScan 4, and has
a link to http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
for Bjoern's InterProScan 45 wrapper.
3. Click the link for Inte
Hi Peter and others,
On Oct 8, 2013, at 10:22 AM, Peter Cock wrote:
> Hi Greg, Jean-Frédéric,
>
> I'm returning to this old thread rather than starting a new one,
> since it is nicely aligned with something I wanted to raise.
>
> On Tue, Feb 19, 2013 at 2:23 PM, Greg Von Kuster wrote:
>> Hel
Peter,
The following wiki page should provide additional information on the
testing environments:
http://wiki.galaxyproject.org/AutomatedToolTests#Automated_testing_framework_processes
I should point out that I have not yet finished decoupling the revisions
of Galaxy and the installation and
On Tue, Oct 8, 2013 at 3:47 PM, Greg Von Kuster wrote:
> Hi Peter and others,
>
>Peter wrote:
>> As an aside, I've asked before about why the function tests look
>> at *.loc rather than *.loc.sample and not had a clear answer.
>
> The functional tests look at .loc files because they will have unco
On Tue, Oct 8, 2013 at 3:57 PM, Dave Bouvier wrote:
> Peter,
>
> The following wiki page should provide additional information on the testing
> environments:
>
> http://wiki.galaxyproject.org/AutomatedToolTests#Automated_testing_framework_processes
>
> I should point out that I have not yet finish
Hi Peter,
On Oct 8, 2013, at 11:01 AM, Peter Cock wrote:
> On Tue, Oct 8, 2013 at 3:47 PM, Greg Von Kuster wrote:
>> Hi Peter and others,
>>
>> Peter wrote:
>>> As an aside, I've asked before about why the function tests look
>>> at *.loc rather than *.loc.sample and not had a clear answer.
>
Peter,
Thanks for the followup report, I've committed a fix for that issue in
10838:c0f049223e27.
--Dave B.
On 10/08/2013 06:18 AM, Peter Cock wrote:
Title was: [galaxy-iuc] Platform-specific tool dependency support has
been enhanced.
On Fri, Oct 4, 2013 at 6:08 PM, Dave Bouvier wrote:
Peter,
Yes, the testing framework needs to be maintained independently, in
order to allow for enhancements to the test scripts without affecting
the stable Galaxy that is instantiated by these scripts.
--Dave B.
On 10/08/2013 11:05 AM, Peter Cock wrote:
On Tue, Oct 8, 2013 at 3:57 PM, Da
On Tue, Oct 8, 2013 at 4:23 PM, Dave Bouvier wrote:
> Peter,
>
> Thanks for the followup report, I've committed a fix for that issue in
> 10838:c0f049223e27.
>
>--Dave B.
Thank you - fingers crossed for the test run tonight :)
Peter
___
On Tue, Oct 8, 2013 at 4:13 PM, Greg Von Kuster wrote:
>>> I don't agree with this - the sample files should be used as guidance for
>>> the admin to create functionally correct .loc files. This is the same
>>> aopproach used for all Galaxy .sample files ( e.g., universe_wsgi.ini.sample
>>> <-> u
Hi,
After the last update I'm getting the following error.
The job is submitted to SGE e executed, but galaxy doesn't get the result
and keeps showing the job is executing (yellow box).
Any clues?
Thanks,
Adhemar
galaxy.jobs.runners ERROR 2013-10-08 13:01:18,488 Unhandled exception
checking acti
In order to test that, I've just downloaded a new galaxy-central and
configured it to submit jobs in our SGE cluster. Same problem. The job
starts and finishes, but galaxy keeps informing it's still running.
I've also attached the job_conf.xml file.
Need help, please!
-Adhemar
galaxy.jobs.runners
> I look forward to some more details from Dan on *.loc
> file setup.
Hi Peter, Dan and all,
What a timely discussion! I am just in the process of setting up loc files for
some new indexes I have created (bowtie2, etc), and would really like to see
this automated.
I see there is a Galaxy scri
Dear Galaxy developers,
Currently our production Galaxy runs the stable branch. However, I see one or
two reasons to want to run the development (default) branch for a while.
This will involved migrating the database to a later version, which is fine, as
migration scripts exists.
What I am wo
Peter, Björn,
I have restored gfortran to the repository test host. I believe it was
inadvertently removed, possibly as a side effect of updating packages or
removing packages that were causing conflicts with the Galaxy eggs.
Numpy and biopython should now install successfully, as they do in m
On Tue, Oct 8, 2013 at 4:32 PM, Guest, Simon
wrote:
> What I am wondering is whether it is guaranteed that I will be able to get
> back onto stable at a later date, i.e. there will be a database migration
> path from whatever development database version I end up on, onto a future
> stable data
Hi Theresa,
The clusters have been on and off for most of the last few weeks. The
updated server is now up and much faster! We are actively seeking feedback.
If a job did end up failing due to a cluster or fileserver issue during
the move, then please just re-run it. There could be many contr
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