> Date: Wed, 25 Jun 2014 07:49:36 -0500
> Subject: Re: [galaxy-dev] Run a tool's workflow one by one ?
> From: jmchilton@gmail.com
> To: leonardsquall15@hotmail.com
> CC: galaxy-dev@lists.bx.psu.edu
>
> There was a problem with the config I sent you - it defines two
> destinations for jobs but doesn't specify a default. I have updated
> the gist (and actually tried loading it in Galaxy this time):
> https://gist.github.com/jmchilton/ff186b01d51d401623be. Hope this
> helps you make progress on this issue.
>
> -John
>
> On Wed, Jun 25, 2014 at 2:09 AM, Pat-74100 <leonardsquall15@hotmail.com> wrote:
> > Hi John
> >
> > Thanks for your reply.
> > I've copied your job_conf.xml.
> >
> > Unfortunately, I've got an error when I ran run.sh:
> >
> > galaxy.jobs DEBUG 2014-06-25 09:06:17,610 Loading job configuration from
> > ./job_conf.xml
> > galaxy.jobs DEBUG 2014-06-25 09:06:17,610 Read definition for handler 'main'
> > galaxy.jobs INFO 2014-06-25 09:06:17,610 Setting <handlers> default to child
> > with id 'main'
> > Traceback (most recent call last):
> > File
> > "my_repertory/galaxy-python/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
> > line 39, in app_factory
> > app = UniverseApplication( global_conf = global_conf, **kwargs )
> > File "my_repertory/galaxy-python/galaxy-dist/lib/galaxy/app.py", line 64,
> > in __init__
> > self.job_config = jobs.JobConfiguration(self)
> > File
> > "my_repertoryr/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> > 107, in __init__
> > self.__parse_job_conf_xml(tree)
> > File "my_repertory/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py",
> > line 177, in __parse_job_conf_xml
> > self.default_destination_id = self.__get_default(destinations,
> > self.destinations.keys())
> > File my_repertoryr/galaxy-python/galaxy-dist/lib/galaxy/jobs/__init__.py",
> > line 300, in __get_default
> > raise Exception("No <%s> default specified, please specify a valid id or
> > tag with the 'default' attribute" % parent.tag)
> > Exception: No <destinations> default specified, please specify a valid id or
> > tag with the 'default' attribute
> >
> >
> > I don't understand where is the problem.
> >
> > Pat
> >
> >> Date: Mon, 23 Jun 2014 22:19:27 -0500
> >> Subject: Re: [galaxy-dev] Run a tool's workflow one by one ?
> >> From: jmchilton@gmail.com
> >> To: leonardsquall15@hotmail.com
> >> CC: galaxy-dev@lists.bx.psu.edu
> >
> >>
> >> Its looks like you were going to post an error message but didn't.
> >> That might help debug problem.
> >>
> >> There is no way currently at the workflow level to force one job to
> >> wait for another before completion (other than assigning an explicit
> >> input/output relationship between the steps). There is a Trello card
> >> for this here https://trello.com/c/h5qZlgU8.
> >>
> >> I am not sure that Trello card is really the best approach for this
> >> problem though. If it really is the case that these jobs can run
> >> simultaneously and they are not implicitly dependent on each other in
> >> some way not represented in the workflow - than it is likely they are
> >> running on a machine that just doesn't have enough resources (likely
> >> memory) to run these properly. The correct solution for this I think
> >> should be properly configuring a job_conf.xml file to not let Galaxy
> >> tools over consume memory.
> >>
> >> By default Galaxy will run 4 jobs simultaneously - any job of any time
> >> - regardless of memory consumption, threads used, etc.... This gist
> >> (https://gist.github.com/jmchilton/ff186b01d51d401623be) contains a
> >> job_conf.xml that you can stick in your Galaxy root directory to
> >> ensure a handful of tools (I used ids hilbert, fft, slm as example ids
> >> but you should replace these values with actual values of your tool)
> >> can only run one job at a time. All other jobs will continue t
> >> concurrently run two at a time beside these.
> >>
> >> If you are using a distributed resource manager (like sun grid engine,
> >> SLURM, Condor, etc...) then the solution is a little different. You
> >> should assign these tools to job destination that consume a whole node
> >> - you would to provide more information about the cluster hardware and
> >> software configuration for me to provide an example of this.
> >>
> >> Beside that the common advice about scaling up Galaxy holds - you
> >> should configure Postgres instead of sqlite, setup a proxy (nginx or
> >> Apache), disable debug in universe_wsgi.ini, etc.... See
> >> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
> >> for details. All of these things can help in situations like this.
> >>
> >> -John
> >>
> >>
> >>
> >>
> >> On Mon, Jun 23, 2014 at 11:22 AM, Pat-74100 <leonardsquall15@hotmail.com>
> >> wrote:
> >> > Hi !
> >> >
> >> > I have a big workflow and sometime when I launched it, I got an error
> >> > message for some of my tools : unable to finish job.
> >> > I think it's maybe Galaxy ran multiple job so I get this error message.
> >> >
> >> > I'm looking to run my workflow "step by step".
> >> >
> >> > For example this workflow:
> >> >
> >> > http://hcsvlab.org.au/wp-content/uploads/2014/02/PsySoundTest1.png
> >> >
> >> > I'm looking to run Hilbert THEN FFT THEN SLM and no Hilbert, FFT and SLM
> >> > at
> >> > the same time.
> >> >
> >> > Is it possible to make a workflow which wait to finish a job before run
> >> > an
> >> > another job ?
> >> >
> >> > Thanks
> >> >
> >> > ___________________________________________________________
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