Commit 4d25aed0 authored by Amir MOHAMMADI's avatar Amir MOHAMMADI
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Merge branch '20-logs-are-not-kept-when-a-file-with-the-same-name-as-the-logs-folder-name-exists' into 'master'

Resolve "Logs are not kept when a file with the same name as the logs folder name exists"

See merge request !16
parents a9b5d476 7ddc9d33
Pipeline #14677 passed with stages
in 11 minutes and 13 seconds
......@@ -11,7 +11,7 @@ from __future__ import print_function
from .manager import JobManager
from .setshell import environ
from .models import add_job, Job
from .tools import logger, qsub, qstat, qdel, make_shell
from .tools import logger, qsub, qstat, qdel, make_shell, makedirs_safe
import os, sys
......@@ -58,6 +58,10 @@ class JobManagerSGE(JobManager):
dependent_jobs = self.get_jobs(dependencies)
deps = sorted(list(set([ for j in dependent_jobs])))
# make sure log directory is created and is a directory
assert os.path.isdir(job.log_dir), "Please make sure --log-dir `{}' either does not exist or is a directory.".format(job.log_dir)
# generate call to the wrapper script
command = make_shell(python, [jman, '-d%s' % ('v'*verbosity), self._database, 'run-job'])
q_array = "%d-%d:%d" % array if array else None
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