I always see this error pop up in the logs when one of the steps failed...
It seems to have a problem deleting the working directory since it claims they are not empty.
Ofcourse when I check, the directory is empty, but I am left with a gazilion empty working directories, alhtough no problems with the installation otherwise...
Using the latest pull
galaxy.datatypes.metadata DEBUG 2012-11-08 15:43:29,532 Cleaning up external metadata files
galaxy.objectstore CRITICAL 2012-11-08 15:43:29,621 /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/105 delet
e error [Errno 39] Directory not empty: '/mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/105'
ls -la /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/105
drwxrwsr-x 2 svcgalaxy 0 Nov 8 15:42 .
drwxrwsr-x 30 svcgalaxy 565 Nov 8 15:42 ..
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