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: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<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>






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