Hi Steven,
For a quick first pass, have you taken a look at https://github.com/
galaxyproject/galaxy/blob/dev/client/README.md?
Thanks for using Galaxy,
Dan
On Thu, Jul 6, 2017 at 10:11 PM, Steven Shen wrote:
> Hi everyone,
>
> I want to make some change for my local galaxy web, actually I c
Hi Steven,
we have collected a few tutorials and slides here:
http://galaxyproject.github.io/training-material/topics/dev/
especially this:
https://galaxyproject.github.io/training-material//topics/dev/tutorials/webhooks/tutorial.html
and this:
https://galaxyproject.github.io/training-materia
Hi Christopher,
you can increase the JVM memory options via the job_conf.xml file for a
particular tool.
Hope this helps,
Bjoern
Am 06.07.2017 um 13:05 schrieb Previti:
> Dear all,
> I seemly have a java issue (out of memory) when trying to construct a
> picard index for the rat (rn6) genome bui
Code looks interesting. This is for Univa Grid Engine?
In terms of the upload jobs, are those not designed to be run as 'local'
jobs and not with the 'real user' setting?
On Fri, 7 Jul 2017 at 17:32 Matthias Bernt wrote:
> Dear list,
>
> I have implemented a new DRMAA job runner allows to detec
Good afternoon,
Thank you for that! I will look in to it!
Best Regards,
David Jacob Meltzer
From: Nate Coraor
Date: Friday, July 7, 2017 at 5:02 PM
To: David Meltzer
Cc: Yvan Le Bras , "galaxy-dev@lists.galaxyproject.org"
Subject: Re: [galaxy-dev] ustacks - bad interpreter
Hi David,
You ma
Hi David,
You may want to have a look at the first line of:
/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py
The shell is claiming it is:
#!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs
Dear list,
I have implemented a new DRMAA job runner allows to detect runtime and
memory violations. This is done by using the drmaa library functions
job_info + wait or as fallback the commandline tools qstat + qacct. This
has the additional advantage that the runner works also in setups usin
Hi,
I'm trying to run tests against my galaxy server.
I'm using:
./run_tests.sh --external_url my.server.example --external_master_key somekey
To my understanding, this should run functional tests against my server.
However, my server doesn't see any traffic at all.
I can log into my Galaxy Se
Good afternoon,
I will do my best!
Best Regards,
David
From: Yvan Le Bras
Date: Friday, July 7, 2017 at 1:06 PM
To: David Meltzer ,
"galaxy-dev@lists.galaxyproject.org"
Subject: RE : [galaxy-dev] ustacks - bad interpreter
No problem, I was not writing my question clearly...
I suspect a pb w
No problem, I was not writing my question clearly...
I suspect a pb with the stacks_summary related script... Can you investigate
it, I unfortunately can't work on it for now. .. Maybe ""just"" a missing
python interpreter invocation somewhere. .. when executing stacks_summary. ...
---
Good afternoon,
I apologize. I misunderstood the question. Yes, stacks_summary has been
installed correctly as have stacks and velvet.
Additionally, the tool is outputting three items into the history -
Summary from Stacks – red (error)
Ustacks.log – red (error)
Stacks from Data – green (succes
Good afternoon,
I am sorry. I don’t see a tool called stacks_summary installed on my system or
available on the toolshed.
Best Regards,
David
From: Yvan Le Bras
Date: Friday, July 7, 2017 at 12:08 PM
To: David Meltzer ,
"galaxy-dev@lists.galaxyproject.org"
Subject: RE : [galaxy-dev] ustacks
Hi David,
A pb with stacks_summary apparently... and ustacks is working well
apparently... Can you check you have stacks_summary well installed ? I think it
is but there is a pb using it...
Cheers,
Yvan
Envoyé depuis mon appareil Samsung
Message d'origine
De : David Me
Good morning,
I have a user attempting to run ustacks. They are receiving the following error
Fatal error: Exit code 126 (Error in Stacks execution)
/home/big_galaxy/galaxy/database/jobs_directory/079/79363/tool_script.sh:
/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac
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