On Tue, Sep 18, 2012 at 7:11 PM, Scott McManus scottmcma...@gatech.edu wrote:
Sorry - that's changeset 7714:3f12146d6d81
-Scott
Hi Scott,
The good news is this error does seem to be fixed as of that commit:
TypeError: check_tool_output() takes exactly 5 arguments (4 given)
The bad news is
Odd, it works for me on EC2/Cloudman.
jorrit
On 09/19/2012 03:29 PM, Peter Cock wrote:
On Tue, Sep 18, 2012 at 7:11 PM, Scott McManus scottmcma...@gatech.edu wrote:
Sorry - that's changeset 7714:3f12146d6d81
-Scott
Hi Scott,
The good news is this error does seem to be fixed as of that
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
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
I have to admit that I'm a little confused as to why you would
be getting this error at all - the job variable is introduced
at line 298 in the same file, and it's used as the last variable
to check_tool_output in the changeset you pointed to.
(Also, thanks for pointing to it - that made
Is it possible that you are looking at different classes? TaskWrapper's
finish method does not use the job variable in my recently merged code
either (line ~1045), while JobWrapper's does around line 315.
cheers,
jorrit
On 09/18/2012 03:55 PM, Scott McManus wrote:
I have to admit that I'm
Thanks, Jorrit! That was a good catch. Yes, it's a problem with the TaskWrapper.
I'll see what I can do about it.
-Scott
- Original Message -
Is it possible that you are looking at different classes?
TaskWrapper's
finish method does not use the job variable in my recently merged
On Tue, Sep 18, 2012 at 3:09 PM, Jorrit Boekel
jorrit.boe...@scilifelab.se wrote:
Is it possible that you are looking at different classes? TaskWrapper's
finish method does not use the job variable in my recently merged code
either (line ~1045), while JobWrapper's does around line 315.
Ok - that change was made. The difference is that the change
is applied to the task instead of the job. It's in changeset
7713:bfd10aa67c78, and it ran successfully in my environments
on local, pbs, and drmaa runners. Let me know if there are
any problems.
Thanks again for your patience.
Sorry - that's changeset 7714:3f12146d6d81
-Scott
- Original Message -
Ok - that change was made. The difference is that the change
is applied to the task instead of the job. It's in changeset
7713:bfd10aa67c78, and it ran successfully in my environments
on local, pbs, and drmaa
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