Re: [galaxy-dev] maximum value for local_job_queue_workers

2011-02-25 Thread hari krishna
Hi Nate, Thanks for ur reply. I have made a job runner which will submit job to job meta-scheduler, which can handle 200 jobs concurrently. So is it safe to set local_job_queue_workers = 200 ?? This instance of Galaxy will be accessed by some 50 users. So can threadpool_workers be set to 50??

Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster

2011-02-25 Thread Sonali Amonkar
Hi Nate, We are still awaiting any replies to the error on the Torque community. About the debugging, we did try tracejob, however since the job was not getting submitted itself, Torque did not have any logging to the job(it wasn't even a job yet). Meanwhile, we are retrying deployment of

Re: [galaxy-dev] Local Galaxy implimentation

2011-02-25 Thread Anton Nekrutenko
Lee: I am CC'ing you e-mail to galaxy-dev list. You can get a lot of useful answers by posting to this list. Maintaining Galaxy is not different from maintaining other software resources. To run it locally you will need to have a system administration supervision as with any other high

Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster

2011-02-25 Thread Nate Coraor
Sonali Amonkar wrote: Hi Nate, We are still awaiting any replies to the error on the Torque community. About the debugging, we did try tracejob, however since the job was not getting submitted itself, Torque did not have any logging to the job(it wasn't even a job yet). Meanwhile, we

Re: [galaxy-dev] Only use filepaths and Copy data into Galaxy?

2011-02-25 Thread Nate Coraor
Jean-Baptiste Denis wrote: Hello everybody, i've got one galaxy server running. The ressource on the wiki are very useful for that purpose, thank you. I've got one question regarding data library when using upload files from filesystem paths. There is a checkbox, unchecked by default,

Re: [galaxy-dev] Only use filepaths and Copy data into Galaxy?

2011-02-25 Thread Jean-Baptiste Denis
On 02/25/2011 04:20 PM, Nate Coraor wrote: Hi Jean-Baptiste, This is certainly a concern. It's not possible to do this without some hackery, but it's minor hackery. If you're certain you'll never want to have that box unchecked, you can make the following change to

Re: [galaxy-dev] Local Galaxy implimentation

2011-02-25 Thread Hans-Rudolf Hotz
Hi Lee * What is a realistic amount of someones time to implement Galaxy on a Linux server so that it can be used by researchers using the Web? Galaxy is simple to set up and works out-of-the-box. You will have a functional Galaxy server within minutes (yes, 'within minutes').

Re: [galaxy-dev] Local Galaxy implimentation

2011-02-25 Thread Nate Coraor
Hi Lee, If setting up Galaxy on an existing supported cluster, I would estimate the setup time for an experienced sysadmin to be a day or two, although that number can be larger if a lot of tools that depend on external binaries (e.g. NGS mappers) and locally cached reference genomes are desired,

Re: [galaxy-dev] Amazon cloud formation for galaxy

2011-02-25 Thread Enis Afgan
Yeah, also that is is pretty much how CloudMan handles the infrastructure management now - it has it's own descriptor (i.e., template) and from there it handles all the provisioning and coordination of the underlying resources. Granted, having Amazon do it would add to the robustness of the

Re: [galaxy-dev] stagingin and stagingout at DRMAA

2011-02-25 Thread Nate Coraor
hari krishna wrote: Hi , Can any one help me how to transfer files from head node to remote location by using DRMAA job template attributes with example will DRMAA supports staging in and staging out of files,... Hi, You can use the drmaa_transfer_files job template attribute,

Re: [galaxy-dev] unable to login user to local instance

2011-02-25 Thread Nate Coraor
Peter Cock wrote:  File /home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py, line 29    return (content if len(content) = length else content[:length].rsplit(' ', 1)[0]+suffix)                     ^ SyntaxError: invalid syntax I deduce you're using Python 2.4,