We found a problem when we execute a job in local mode with galaxy. When a
job is running and galaxy restarted, we obtain this error : message:
socket.error: [Errno 98] Address already in use
All the file descriptors are passed from parent to child by default with
subprocess.popen. If you want to close all file descriptors excepted
stdin, stdout and stderr, you have to use the option:
close_fds = True.
In local.py line 84-90:
proc = subprocess.Popen( args = command_line, shell = True, cwd =
job_wrapper.working_directory, stdout = stdout_file, stderr = stderr_file,
env = os.environ, preexec_fn = os.setpgrp, close_fds = True )

I hope this will help resolving this bug
Thank you in advance.


Fabien Mareuil

Fabien Mareuil | Centre d'Informatique pour la Biologie
fabien.mare...@pasteur.fr | Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France

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