Hi All,
Thanks to this email[1] from Peter Cock I was able to find what was causing the error I initially described here[2]. I also now have a theory of why this is happening.
My unconfirmed guess. When a colon is present in the standard output or standard error file, someone betweent Galaxy, python-drmaa, pbs-drmaa, Torque or Maui recognize this as a scp syntax, like: user@host:/path/to/file
And then choose to at 'galaxy@' in from of what is really a filesystem path. This is why I'm seeing this kind of error: Unable to copy file /var/spool/torque/spool/1013.head.OU to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmout *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.OU
By using Peter's ".replace(":", "_")" trick on "lib/galaxy/jobs/runners/drmaa.py" I was able to make this issue go away. As Peter mention this is a very dirty fix and I'm sure there has to be a much cleaner way of fixing this issue.
[1]http://dev.list.galaxyproject.org/Galaxy-with-Univa-Grid-Engine-UGE-instead-... [2]http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-t...
I'll be opening a ticket on Trello to follow the progress on this issue. Regards, Carlos