[galaxy-dev] /tmp directory

[Nate Coraor]

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