Thanks for the answer! I've copied this response to the dev list email instead, after realizing its probably best there.
I'm also having some trouble getting our PBS system configured. I have pbs://hostname/ as my pbs parameter in the universe file, as well as everything else specified in the documentation. I'm getting no error in the interface, and the backend never actually gets the job. The error I see in the logs says:
galaxy.jobs.runners.pbs ERROR 2009-10-30 13:40:27,762 Uncaught exception queueing job Traceback (most recent call last): File "/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 144, in run_next self.queue_job( obj ) File "/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 219, in queue_job script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_fnames), self.app.config.pbs_stage_path, exec_dir, command_line) TypeError: sequence item 1: expected string, DatasetPath found
I'm guessing this has something to do with my config parameters, and the queue its trying to submit to. the pbs://hostname/ value was used under the assumption that it would default to the 'default' queue on our cluster, so I'm wondering if I need to hard code those values into the connection string? I'm a little confused as to how the syntax translates to the actual required string. My guess is, for our values:
pbs://variome.chop.edu/default
Perhaps its related to the scrambling of the egg instead? I simply passed LIBTORQUE_DIR to the directory containing my libtorqure.so etc...
? Thanks in advance.
Juan Perin
On Fri, Oct 30, 2009 at 12:07 PM, Nate Coraor nate@bx.psu.edu wrote:
Juan Perin wrote:
I'm hosting galaxy locally and am trying to figure out how to change the
temporary upload location of files from the root / /tmp folder to something else. My /tmp partition is too small to handle large fastq files and this is causing me problems. I see where to change things in the universe file, but that's the final location, not the temporary space.
Hi Juan,
A quick solution is to set $TEMP in your shell environment. In the future, we'll force uploads to honor new_file_path in universe_wsgi.ini.
--nate