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:li...@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: icho...@illumina.com > Website: 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/ > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
