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 ) ) 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<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/