Hi Gordon
This looks very nice - Thank you very much! - and it could replace our
"access permission wrappers" we use for some of our tools.
If I find some time, I will try it on one of our test/development server
and look into an extension to get the permissions from file/database.
Regards
Hi,
I created an XML file for a tool. This tool has an Nexus input. When I click
the input field of the web interface for this tool, it shows all kinds of
data that I can select. How do I restrict the list to show only data in
nexus format? I added a line in the registration part and the sniffer p
We have configured galaxy to work with our SGE cluster using drmaa job runner
interface. We are using 'unified method' for this install and
both TEMP environment variable and new_file_path in universe_wsgi.ini file have
been configured correctly. However, we are seeing some errors where local /
Hi,
I've noticed a ticket on the wiki for per-user tool permissions:
https://bitbucket.org/galaxy/galaxy-central/issue/269/use-galaxy-security-to-restrict-tool
If anyone is interested, the following patch implements such thing (but
requires manual code changes whenever the access needs to be cha
Hello Somayyeh,
These data are from the same authors/release build. At Ensembl, the same
5 core chromosomes plus an additional 78 unplaced scaffolds are
available. The data authors decided not to include these scaffolds in
their publication at NCBI.
For a primary genome, I suggest that we us
yup, works. thanks for the prompt reply
On Thu, Jul 21, 2011 at 10:15 AM, Kanwei Li wrote:
> Fixed on trunk, thanks for reporting!
>
> K
>
> On Thu, Jul 21, 2011 at 12:41 PM, Edward Kirton wrote:
>
>>
>> URL: https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8
>> Module paste.except
Hello Assaf,
I've added this to the ~/contrib directory in change set 5820:c609c2574c66.
Thanks very much for contributing this.
Greg Von Kuster
On Jul 19, 2011, at 2:45 PM, Assaf Gordon wrote:
> Hi all,
>
> I got around to writing the report I always needed: how much time each job
> actual
Hello Christoph,
This is the result of a bug that I've corrected in change set
5819:0f15591f2acd, which should be available in our main Galaxy instance, as
well as the distribution, within the next few weeks. Thanks for pointing this
out, and very sorry for the inconvenience.
Greg Von Kuster
Fixed on trunk, thanks for reporting!
K
On Thu, Jul 21, 2011 at 12:41 PM, Edward Kirton wrote:
>
> URL: https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8
> Module paste.exceptions.errormiddleware:*143* in __call__
> Module paste.debug.prints:*98* in __call__
> Module paste.wsgilib:
URL: https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8
Module paste.exceptions.errormiddleware:*143* in __call__
Module paste.debug.prints:*98* in __call__
Module paste.wsgilib:*539* in intercept_output
Module paste.recursive:*80* in __call__
Module paste.httpexceptions:*632* in __call
Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful !
I wonder how this approach will work out when one runs galaxy as advised
in a production setting:
http://usegalaxy.org/production
Together with the gordon patch to run drmaa as different users:
http://wiki.g2.bx.psu.edu/Event
We are using environment modules ( http://modules.sourceforge.net/ ) on the
cluster and took same approach for the galaxy install. The module files are
loaded using .bashrc file of galaxy user. It's also useful for non-galaxy
users/admins for running galaxy-tools from command-line by simply loa
Jack,
Thanks for following up on this issue. I've fixed the problem in galaxy-central
changeset c176363cb7b2:
https://bitbucket.org/galaxy/galaxy-central/changeset/c176363cb7b2/
Finally, please send all emails to our mailing lists rather than individual
Galaxy developers or other list members.
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