Hallo every one,
I am new to Galaxy, I have a idea which maybe not new to people here. I work
on arabidopsis. maybe you know that UCSC do not offer the genome assembly
so i will install UCSC locally and built the genome assembly for
arabidopsis. this work is half done now.
I also installed Galaxy, if i understand correctly, Galaxy has the link to
UCSC so the user can get data from UCSC. since what i interested is
arabidopsis information, I hope Galaxy can retrive data form the locally
installed UCSC in future. I do not know if it is possible to make this idea
come ture.maybe some of you have done it. if yes, I am gratefully if you
can tell me the how to get it.
I have another question regarding the local job scheduler:
Is it possible to limit the number of jobs *per user* ?
That is - any given user can have up to X number of jobs running
concurrently, regardless of the value of local_job_queue_workers ?
Imagine the following situation:
local_job_queue_worker = 5
Which means that at any given moment, galaxy can run only five jobs.
Now, Galaxy is completely Idle, no jobs are running.
One users starts 7 very long running jobs (each jobs will take about two
If I understand correctly - since no jobs are running, 5 of the user's
job will be started immediately, even with the round-robin policy, right ?
And this means that for the next two hours, every other user which
starts a job - his/her job will be either new or limbo-running, but none
will actually be started, right ?
I think I'm experiencing this situation on my galaxy server.
Users are complaining their jobs have been running 'forever' or not even
starting for a long long time.
Close examination shows that there are running 5 jobs (all from the same
user) which have been running for three hours, and they are kind of
hogging all the worker threads.
To make a long story short -
I would like to make sure a single user can't hog Galaxy.
Is it possible with the local job runner, and if not - is it possible
with the SGE job runner ?
Thanks for reading so far,