Re: [galaxy-dev] drmaa module does not load
Le 27/03/2012 11:03, Louise-Amélie Schmitt a écrit : Le 26/03/2012 16:13, Nate Coraor a écrit : On Mar 26, 2012, at 5:11 AM, Louise-Amélie Schmitt wrote: Hello everyone, I wanted to start the drmaa job runner and followed the instructions in the wiki, but I have this error message when I start Galaxy: galaxy.jobs ERROR 2012-03-23 15:28:49,845 Job runner is not loadable: galaxy.jobs.runners. drmaa Traceback (most recent call last): File "/g/funcgen/galaxy/lib/galaxy/jobs/__init__.py", line 1195, in _load_plugin module = __import__( module_name ) ImportError: No module named drmaa I checked /g/funcgen/galaxy/lib/galaxy/jobs/runners and it contains the drmaa.py file There was no drmaa egg so I made a copy of it from our other Galaxy install but it didn't solve the problem. I don't really know where to start looking, any idea? Thanks, L-A Hi L-A, There's an errant space in the runner name: ' drmaa'. I am going to guess that your start_job_runners looks like: start_job_runners = pbs, drmaa Only the whitespace at the beginning and end of that parameter is stripped. I've committed a fix for this that'll be in the next galaxy-dist, but in the meantime, remove the space after the comma and the drmaa runner should load. --nate Hi Nate, After a removing the space (and a facepalm) it now fetches the drmaa egg and starts the module properly, thanks a lot! I still have an issue though: When I use the run shell script Galaxy crashes right before loading the drmaa runner (right after the pbs runner is loaded). The weird thing is that when I launch the command manually it works fine: python ./scripts/paster.py serve universe_wsgi.runner.ini --server-name=runner0 --pid-file=runner0.pid --log-file=runner0.log --daemon The other weird thing is that I get no error message at all. I'll try looking into it but if you have any idea about what's going wrong, it would help greatly :) Thanks again, L-A ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Ok it looks like I didn't notice the changes in the start scripts and since we use two custom copies of run.sh the code was outdated. I corrected that and it now seems to work properly. Best, L-A ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] drmaa module does not load
Le 26/03/2012 16:13, Nate Coraor a écrit : On Mar 26, 2012, at 5:11 AM, Louise-Amélie Schmitt wrote: Hello everyone, I wanted to start the drmaa job runner and followed the instructions in the wiki, but I have this error message when I start Galaxy: galaxy.jobs ERROR 2012-03-23 15:28:49,845 Job runner is not loadable: galaxy.jobs.runners. drmaa Traceback (most recent call last): File "/g/funcgen/galaxy/lib/galaxy/jobs/__init__.py", line 1195, in _load_plugin module = __import__( module_name ) ImportError: No module named drmaa I checked /g/funcgen/galaxy/lib/galaxy/jobs/runners and it contains the drmaa.py file There was no drmaa egg so I made a copy of it from our other Galaxy install but it didn't solve the problem. I don't really know where to start looking, any idea? Thanks, L-A Hi L-A, There's an errant space in the runner name: ' drmaa'. I am going to guess that your start_job_runners looks like: start_job_runners = pbs, drmaa Only the whitespace at the beginning and end of that parameter is stripped. I've committed a fix for this that'll be in the next galaxy-dist, but in the meantime, remove the space after the comma and the drmaa runner should load. --nate Hi Nate, After a removing the space (and a facepalm) it now fetches the drmaa egg and starts the module properly, thanks a lot! I still have an issue though: When I use the run shell script Galaxy crashes right before loading the drmaa runner (right after the pbs runner is loaded). The weird thing is that when I launch the command manually it works fine: python ./scripts/paster.py serve universe_wsgi.runner.ini --server-name=runner0 --pid-file=runner0.pid --log-file=runner0.log --daemon The other weird thing is that I get no error message at all. I'll try looking into it but if you have any idea about what's going wrong, it would help greatly :) Thanks again, L-A ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] drmaa module does not load
On Mar 26, 2012, at 5:11 AM, Louise-Amélie Schmitt wrote: > Hello everyone, > > I wanted to start the drmaa job runner and followed the instructions in the > wiki, but I have this error message when I start Galaxy: > > galaxy.jobs ERROR 2012-03-23 15:28:49,845 Job runner is not loadable: > galaxy.jobs.runners. drmaa > Traceback (most recent call last): > File "/g/funcgen/galaxy/lib/galaxy/jobs/__init__.py", line 1195, in > _load_plugin > module = __import__( module_name ) > ImportError: No module named drmaa > > I checked /g/funcgen/galaxy/lib/galaxy/jobs/runners and it contains the > drmaa.py file > > There was no drmaa egg so I made a copy of it from our other Galaxy install > but it didn't solve the problem. > > I don't really know where to start looking, any idea? > > Thanks, > L-A Hi L-A, There's an errant space in the runner name: ' drmaa'. I am going to guess that your start_job_runners looks like: start_job_runners = pbs, drmaa Only the whitespace at the beginning and end of that parameter is stripped. I've committed a fix for this that'll be in the next galaxy-dist, but in the meantime, remove the space after the comma and the drmaa runner should load. --nate ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
