Hi Pete, Your subject says you are unable to build pbs_python using scramble. Could you provide details on what's not working there?
Galaxy is not going to work with a different version of pbs_python unless a bit of hacking is done to make it attempt to do so. We test Galaxy with specific versions of its dependencies, which is why we control the versions of those dependencies and provide the scramble script to (hopefully) make it painless to build them yourself, should it be necessary to do so, as is always the case with pbs_python. --nate On Mon, Mar 3, 2014 at 3:57 PM, Pete Schmitt <peter.r.schm...@dartmouth.edu> wrote: > Following the directions from here: > https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS > > I'm trying to get pbs_python to work as I'm using torque for scheduling > galaxy jobs. > > Note: This is a fresh install of galaxy from galaxy-dist on CentOS 5.10 > > I have pbs_python 4.4.0 module installed into a source-built version of > python/2.7.6 > > I get the following error in the output of run.sh: > > galaxy.jobs INFO 2014-03-03 15:46:45,485 Handler 'main' will load all > configured runner plugins > Traceback (most recent call last): > File > "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/webapps/galaxy/buildapp.py", > line 39, in app_factory > app = UniverseApplication( global_conf = global_conf, **kwargs ) > File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/app.py", line 130, in > __init__ > self.job_manager = manager.JobManager( self ) > File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/manager.py", line > 31, in __init__ > self.job_handler = handler.JobHandler( app ) > File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/handler.py", line > 30, in __init__ > self.dispatcher = DefaultJobDispatcher( app ) > File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/handler.py", line > 568, in __init__ > self.job_runners = self.app.job_config.get_job_runner_plugins( > self.app.config.server_name ) > File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/__init__.py", line > 449, in get_job_runner_plugins > module = __import__( module_name ) > File "/nextgen3/galaxy/galaxy-dist-py27/lib/galaxy/jobs/runners/pbs.py", > line 31, in <module> > raise Exception( egg_message % str( e ) ) > Exception: > > The 'pbs' runner depends on 'pbs_python' which is not installed or not > configured properly. Galaxy's "scramble" system should make this > installation > simple, please follow the instructions found at: > > http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster > > Additional errors may follow: > pbs-python==4.3.5 > > This is the job_conf.xml file: > > <?xml version="1.0"?> > <job_conf> > <plugins> > <plugin id="pbs" type="runner" > load="galaxy.jobs.runners.pbs:PBSJobRunner"/> > </plugins> > <handlers> > <handler id="dirigo"/> > </handlers> > <destinations default="pbs_default"> > <destination id="pbs_default" runner="pbs"/> > <param > id="Resource_List">walltime=72:00:00,nodes=1:ppn=4</param> > </destinations> > </job_conf> > > I did not use the scramble system to install the pbs_python module. I > downloaded the latest version > available and installed it from the root account. > > > -- > > Pete Schmitt > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
