On 2/18/11 2:37 PM, Glen Beane wrote:

On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote:

It turns out the user's environment is not set up for batch jobs,
only the system environment.  I too added ". ~/.bashrc" to
lib/galaxy/jobs/runners/drmaa.py.

I'm afraid this is a kludgy fix that will break if/when the
drmaa.py file gets updated.  It'll work for now, but there has got
to be a better way.


I use TORQUE, but I don't use the drmaa runner.  In my case I have no
problems with setting the PATH in the .bashrc for the galaxy user on
my cluster.  Is there a particular reason why you want to use the
drmaa runner instead of the PBS runner if your cluster uses TORQUE?

I couldn't get the pbs_runner to work...so I went with drmaa.





On 2/18/11 1:30 PM, Zhibin Lu wrote:
Hi,

I had same problem since we do not install software in the
system directory. I had to add PATH into
./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if
anyone has better solution.

Zhibin Lu Bioinformatics Support

Ontario Institute for Cancer Research MaRS Centre, South Tower
101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3

www.oicr.on.ca

Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To:
golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re:
[galaxy-dev] cluster path question

Ryan Golhar wrote:

Ryan Golhar wrote:
I'm setting up Galaxy to run on my cluster using drmaa. I
can see jobs getting submitted to Torque however the jobs
keep failing, because the tools are in the default system
path.

How do I tell galaxy to append a directory to the path
used by jobs?

Hi Ryan,

Whatever user is running the jobs will need to modify the
$PATH in its shell startup files. If you're using bash,
this would probably be ~/.bash_profile

It already is in .bashrc (which is called by .bash_profile)
for the galaxy user. I can submit the script from the shell
and it runs okay so something is up with either how the
galaxy app is submitting the job or the environment being
used by the galaxy job.

When you say submit via the shell, do you mean with qsub, or by
logging in to a node and running the wrapper script?

I haven't tested Torque with the drmaa runner so perhaps it's
submitting in a way which starts the shell in non-interactive,
non-login mode. Let me know if you can determine for certain
that no shell startup files are being read, and I'll try to
replicate this in my environment.

I'd like to modify the job script to print out some
debugging information to determine what environment variables
are set when the job gets executed. Actually, this would be a
useful "tool" within Galaxy to test the cluster.

That's probably the simplest method, to just create a tool that
outputs (either to stdout or the output file) what you'd like
to see.



begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The
Cancer Institute of NJ;Cancer Informatics
Core/Bioinformatics adr:5th floor;;120 Albany St;New
Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu
title:NGS Bioinformatics Specialist tel;work:(732) 235-6613
tel;fax:(732) 235-6267 tel;cell:(732) 236-1176
x-mozilla-html:FALSE url:http://www.cinj.org version:2.1
end:vcard


_______________________________________________ To manage
your subscriptions to this and other Galaxy lists, please
use the interface at:

http://lists.bx.psu.edu/

_______________________________________________ To manage your
subscriptions to this and other Galaxy lists, please
use the interface at:

http://lists.bx.psu.edu/



_______________________________________________ To manage your
subscriptions to this and other Galaxy lists, please use the
interface at:

http://lists.bx.psu.edu/

-- CONFIDENTIALITY NOTICE: This email communication may contain
private, confidential, or legally privileged information intended
for the sole use of the designated and/or duly authorized
recipient(s). If you are not the intended recipient or have
received this email in error, please notify the sender immediately
by email and permanently delete all copies of this email including
all attachments without reading them. If you are the intended
recipient, secure the contents in a manner that conforms to all
applicable state and/or federal requirements related to privacy
and confidentiality of such information.
<golharam.vcf><ATT00001..txt>

-- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207)
288-6153




_______________________________________________ To manage your
subscriptions to this and other Galaxy lists, please use the
interface at:

http://lists.bx.psu.edu/


--
CONFIDENTIALITY NOTICE: This email communication may contain private,
confidential, or legally privileged information intended for the sole
use of the designated and/or duly authorized recipient(s). If you are
not the intended recipient or have received this email in error, please
notify the sender immediately by email and permanently delete all copies
of this email including all attachments without reading them. If you are
the intended recipient, secure the contents in a manner that conforms to
all applicable state and/or federal requirements related to privacy and
confidentiality of such information.

<<attachment: golharam.vcf>>

_______________________________________________
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:

  http://lists.bx.psu.edu/

Reply via email to