I'd like to share a new tool for Galaxy:
Reads a tab-delimited file and produces a cross-tabulation table of two
or more variables.
Sources + XMLs are available here:
Screenshots of the galaxy tool:
There's no limit to the number of input lines -
so this tool can create pivot tables of files with more than one million
lines (which Excel currently can't do).
The tool is free for use.
Comments are welcomed,
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,
I am planning on integrating sequence alignment programs to our local
instance of Galaxy. I was wondering if anyone else has developed
wrappers for the following programs: Maq, Bowtie, Tophat.
Also, is there a central repository for any new tools or wrappers that
have been created by other developers? It would certainly be a useful
resource and if I need to wrap these tools myself I would be happy
share the code.
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