Hi all,
I'm trying to configure Galaxy to talk to our SGE cluster via DRMAA.
I've got jobs submitting, and can verify they are in the queue and then
run via qstat (from the cluster). However, something isn't right.
I'm testing with blastp using the following in universe_wsgi.ini
[galaxy:tool_run
Peter:
I have a working sge setup.
Two ideas:
1 - look in the sge logs on the worker node (on my system they are in
/var/spool...)
2 - maybe a permission problem?
brad
--
Brad Langhorst
New England Biolabs
langho...@neb.com
On 2/2/12 8:50 AM, "Peter Cock" wrote:
>Hi all,
>
>I'm trying
Dear Galaxy Developers
I wish to write set of tools for Galaxy Community; tools will use
Postgresql/MySQL database (other than the default galaxy database). Tool's
dropdown boxes will load values from the database on the fly. I had a look at
tool configuration at Galaxy WiKi and I can't seems t
> Ususally the most important information is the first and last step
> E.g.
> The TopHat run should be called
> TopHat on SOLiD 24A
>
> The alignment stats should be
> SAM/BAM Summary Metrics of Solid 24A
> With the rest of the tools in the chain identified in the "more information"
> box.
>
On Thu, Feb 2, 2012 at 1:54 PM, Langhorst, Brad wrote:
> Peter:
>
> I have a working sge setup.
> Two ideas:
> 1 - look in the sge logs on the worker node (on my system they are in
> /var/spool...)
No sign of any SGE logs there - could be system configuration dependent,
but thanks.
> 2 - maybe a
On Feb 2, 2012, at 8:21 AM, Peter Cock wrote:
On Thu, Feb 2, 2012 at 1:54 PM, Langhorst, Brad
mailto:langho...@neb.com>> wrote:
Peter:
I have a working sge setup.
Two ideas:
1 - look in the sge logs on the worker node (on my system they are in
/var/spool...)
No sign of any SGE logs there - cou
Hi all,
Is there a way, or better yet a coded example, of how to list the options
for an input parameter using the contents of a shared data library? Up
until now I've use Python scripts to get the input file options from a
directory listing for a hardcoded path on the server, but it'd be much n
On Feb 2, 2012, at 10:35 AM, Shantanu Pavgi wrote:
> Peter,
>
> I am having similar issue and it started happening only after the recent
> update. See:
> http://galaxy-development-list-archive.2308389.n4.nabble.com/job-cleanup-files-drmout-and-drmerr-not-found-td4341867.html
>
>
> I haven't
The job scripts generated by galaxy contain following code. I was wondering
what's the purpose of if-block after setting 'GALAXY_LIB="None"' assignment.
{{{
GALAXY_LIB="None"
if [ "$GALAXY_LIB" != "None" ]; then
if [ -n "$PYTHONPATH" ]; then
PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
On Feb 2, 2012, at 12:22 PM, Nate Coraor wrote:
> On Feb 2, 2012, at 10:35 AM, Shantanu Pavgi wrote:
>
>> Peter,
>>
>> I am having similar issue and it started happening only after the recent
>> update. See:
>> http://galaxy-development-list-archive.2308389.n4.nabble.com/job-cleanup-files-drmo
On Feb 2, 2012, at 12:23 PM, Shantanu Pavgi wrote:
>
> The job scripts generated by galaxy contain following code. I was wondering
> what's the purpose of if-block after setting 'GALAXY_LIB="None"' assignment.
>
> {{{
> GALAXY_LIB="None"
> if [ "$GALAXY_LIB" != "None" ]; then
>if [ -n "$PY
Dear galaxy team
thank you a lot for providing a complete solution for biologists to
analyse their data, i have one question about galaxy : i see that
there are a lot of tools for example for ngs, and i could not
understand or find the tool in galaxy directories, is that means that
all the
On Feb 1, 2012, at 9:13 PM, Derrick LIN wrote:
> Hi guys,
>
> Is there anyone has actually setup galaxy on a Rocks based cluster?
>
> I know that galaxy should be hosted on a submission host so that it can
> submit jobs to the cluster.
>
> Rocks provides preconfigured DRM such as SGE, so I st
Hello,
These types of tools are not rewritten, but are instead wrapped so that
they function within the Galaxy framework. Galaxy, dependent tools, and
reference datasets and indexes are all installed separately.
For the basic overview, please see:
http://getgalaxy.org
A list of Tool dependen
If you are using Ubuntu LTS, you can use packages we are developing for Galaxy
dependencies on Bio-linux: https://launchpad.net/~nebc/+archive/galaxy
This list is currently incomplete, but steadily growing. Perhaps what you need
is here already.
Best regards,
Casey
Casey Bergman, Ph.D.
Facu
Hello Ambarish,
On 2/1/12 6:42 PM, ambarish biswas wrote:
Hi,
when I try to fetch sequence for SacCer3 using UCSC Main table Browser,
Are you using "Get Data -> UCSC Main", to access the UCSC Main table
browser and the sacCer3 database? If so, and errors are coming up in the
Table Browser,
Hi,
We've been running into an issue when attempting to create a new toolshed tool.
We have the toolshed and the main galaxy web app setup and running, but
updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial
request
Thanks a lot Jennifer,
Will try what u suggested.
With Regards,
Ambarish Biswas,
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,
Tel: +64(22)0855647
Fax: +64(0)3 479 7866
On Fri, Feb 3, 2012 at 10:21 AM, Jennifer Jackson wrote:
> Hello Ambarish,
Just filed as Issue #714 on bitbucket. I noticed that multiple input seems to
be broken on workflows when selecting more that one file (a single file works).
This is happening on our local instance, using Jan 27 galaxy-dist release, as
well as both main/test.g2.bx.psu.edu Galaxy servers (latte
Can you share a workflow that's failing for you on test with me? I just tried
a simple workflow with nothing but an input and FastQC and ran with multiple
inputs successfully.
Thanks!
Dannon
On Feb 2, 2012, at 11:15 PM, Fields, Christopher J wrote:
> Just filed as Issue #714 on bitbucket.
20 matches
Mail list logo
