Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-19 Thread Peter Cock
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

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-19 Thread Jorrit Boekel
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

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
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

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
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

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Peter Cock
On Tue, Sep 18, 2012 at 2:55 PM, Scott McManus scottmcma...@gatech.edu wrote: 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

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Jorrit Boekel
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

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
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

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Peter Cock
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.

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
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.

Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)

2012-09-18 Thread Scott McManus
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