juan perin wrote:
Thanks for the answer! I've copied this response to the dev list email instead, after realizing its probably best there.
Agreed.
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
Hi Juan, It looks like you're using file staging, and there was a bug in our file staging code (we don't use staging ourselves anymore, so it wasn't caught before). Here's the fix, you can pull it from our central repo or simply apply it manually: http://bitbucket.org/galaxy/galaxy-central/changeset/dac542cca894/ --nate