On Nov 14, 2011, at 2:23 PM, Chorny, Ilya wrote:

I think the problem has to do with self.app.config.outputs_to_working_directory which dos not jive well with linking files from the admin menu instead of uploading them. It still performs the move (i.e) in lib/galaxy/jobs/__init__.py and moves a link to the actual files and writes over it. Any thoughts on how to fix this. Looks like more of a core bug.

if self.app.config.outputs_to_working_directory: for dataset_path in self.get_output_fnames(): try: shutil.move( dataset_path.false_path, dataset_path.real_path ) log.debug( "finish(): Moved %s to %s" % ( dataset_path.false_path, dataset_path.real_path ) )

It looks like the central code encounters this bug as well, not sure how it made it this long. I'm working on it now. --nate

From: Oren Livne [mailto:livne@uchicago.edu] Sent: Friday, November 11, 2011 1:33 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Actual User Code

Check the permissions of the test.bam file. Maybe the galaxy user can't write into a temp directory when it runs the external_chown_script.

On 11/11/2011 3:30 PM, Chorny, Ilya wrote: When I try to link file paths into a shared data library from the admin menu it fails. I get the following in the log file:

galaxy.jobs DEBUG 2011-11-11 13:24:38,280 (2645) Changing ownership of working directory with: /usr/bin/sudo -E /home/galaxy/production/Sept06/galaxy-central/sc ripts/external_chown_script.py ./database/job_working_directory/2645 galaxy 504 galaxy.jobs ERROR 2011-11-11 13:24:38,771 fail(): Missing output file in working directory: [Errno 13] Permission denied: '/bioinfoSD/ichorny/test.bam' galaxy.datatypes.metadata DEBUG 2011-11-11 13:24:38,919 Cleaning up external metadata files

STDOUT has the following :

Job 2645's output dataset(s) could not be read

Also my file get erased:

/bioinfoSD/ichorny/test.bam

Any thoughts?

Thanks,

Ilya

Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com Website: www.illumina.com

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