-------- Original Message -------- Subject: Re: how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini Date: Tue, 13 Aug 2013 23:21:16 -0700 From: tin h <tin6150@gmail.com> To: Jennifer Jackson <jen@bx.psu.edu> CC: Galaxy Dev <galaxy-dev@bx.psu.edu> Thank you Jennifer. I am not sure if my previous email got gabled up... Just to be sure, I specified the following in universe_wsgi.ini default_cluster_job_runner = drmaa://-q default.q -V -v TMPDIR=/scratch/ when i start galaxy, looking at the console log, this is what I see: galaxy.jobs <http://galaxy.jobs> DEBUG 2013-08-14 14:08:14,885 Loaded job runner 'galaxy.jobs.runners.drmaa:DRMAAJobRunner' as 'drmaa' galaxy.jobs.runners.drmaa DEBUG 2013-08-14 14:08:14,885 Converted URL 'drmaa://-q default.q -V -v TMPDIR=/scratch/' to destination runner=drmaa, params={'nativeSpecification': '-q default.q -V -v TMPDIR='} galaxy.jobs <http://galaxy.jobs> DEBUG 2013-08-14 14:08:14,885 Legacy destination with id 'drmaa://-q default.q -V -v TMPDIR=/scratch/', url 'drmaa://-q default.q -V -v TMPDIR=/scratch/' converted, got params: galaxy.jobs <http://galaxy.jobs> DEBUG 2013-08-14 14:08:14,885 nativeSpecification: -q default.q -V -v TMPDIR= The parser has stopped at the / before scratch and ignored the rest :( I did refer to http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster and tried to define job_conf.xml as <?xml version="1.0"?> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> </plugins> <destinations default="sge_default"> <destination id="sge_default" runner="drmaa"> <param id="nativeSpecification">-q default.q -V -v TMPDIR=/scratch</param> </destination> </destinations> </job_conf> But then galaxy won't start, giving me the error of: Traceback (most recent call last): File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 37, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 95, in __init__ self.job_config = jobs.JobConfiguration(self) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 107, in __init__ self.__parse_job_conf_xml(tree) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 157, in __parse_job_conf_xml self.default_handler_id = self.__get_default(handlers, self.handlers.keys()) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 286, in __get_default rval = parent.get('default') AttributeError: 'NoneType' object has no attribute 'get' I am not sure what the "default" refers to, doesn't seems to be the destinations default specified as I tried changing that name but the error message remains the same. Any help so that I can pass TMPDIR=/scratch into SGE qsub would be greatly appreciated. -Tin -- I am riding to fundraise for the Cystic Fibrosis Foundation. Please consider a tax deductible donation at http://www.cff.org/LWC/dsp_DonationPage.cfm?idEvent=23815&idUser=615989 ~~~ __o Engineering is the art of making compromises. ~~~ _ <_ Science is the reverse engineering of the compromises made by nature. ~~~ (_)/(_) Medicine is the hacking of the scientific knowledge base. - A comp sci student :-) On 8/13/13 7:28 PM, Jennifer Jackson wrote:
Hi Tin,
I am going to move this over to the galaxy-dev@bx.psu.edu mailing list (good for local install questions) to give it better viability.
I am by no means the best person to help with this, so hopefully others will jump in, but just from looking at this I am wondering if you shouldn't be instead looking at the " job_conf.xml.sample_advanced" file. There is the default version as well, but it is probably not what you are looking for if you want to add custom logging scripts.
For universe_wsgi.ini, it seems like maybe the problem with the syntax is most likely the unknown "default_cluster_job_runner" variable and the double "=" in the line. Slashes should be fine unescaped here. But as I said, I think the other file is the place for the changes anyway, or maybe both, but using known variables and a single "=" per path.
But let's see what the developers think!
Jen Galaxy team
On 8/12/13 3:49 PM, tin h wrote:
Hello galaxy gurus,Â
I am trying to configure a local galaxy server to submit to SGE using DRMAA, it works, but I would like to specify the equivalent of "-v TMPDIR=/scratch" for qsub.
I tried updating universe_wsgi.ini with something like: Â default_cluster_job_runner = Â drmaa://-q default.q -V -v TMPDIR=/scratch/ but that doesn't work because "/" is a delimiter, and I have not been able to find way to escape it. Â Is there any tricks for this?
Much thanks in advance for your help in this matter. -Tin
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