I'll check it out. Thanks. ----- Original Message ----- > Hi all (and in particular, Scott), > > I've just updated my development server and found the following > error when running jobs on our SGE cluster via DRMMA: > > galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper > finish method failed > Traceback (most recent call last): > File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", > line 371, in finish_job > drm_job_state.job_wrapper.finish( stdout, stderr, exit_code ) > File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line > 1048, in finish > if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): > TypeError: check_tool_output() takes exactly 5 arguments (4 given) > > This looks to have been introduced in this commit: > https://bitbucket.org/galaxy/galaxy-central/changeset/f557b7b05fdd701cbf99ee04f311bcadb1ae29c4#chg-lib/galaxy/jobs/__init__.py > > There should be an additional jobs argument, proposed fix: > > $ hg diff lib/galaxy/jobs/__init__.py > diff -r 4007494e37e1 lib/galaxy/jobs/__init__.py > --- a/lib/galaxy/jobs/__init__.py Tue Sep 18 09:40:19 2012 +0100 > +++ b/lib/galaxy/jobs/__init__.py Tue Sep 18 10:06:44 2012 +0100 > @@ -1045,7 +1045,8 @@ > # Check what the tool returned. If the stdout or stderr > matched > # regular expressions that indicate errors, then set an > error. > # The same goes if the tool's exit code was in a given > range. > - if ( self.check_tool_output( stdout, stderr, tool_exit_code > ) ): > + job = self.get_job() > + if ( self.check_tool_output( stdout, stderr, tool_exit_code, > job ) ): > task.state = task.states.OK > else: > task.state = task.states.ERROR > > > (Let me know if you want this as a pull request - it seems a lot of > effort for a tiny change.) > > Regards, > > Peter > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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