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
for details. All of these things can help in situations like this.
On Mon, Jun 23, 2014 at 11:22 AM, Pat-74100 <leonardsqual...@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:
> 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 ?
> 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:
> To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at: