On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison firstname.lastname@example.org wrote:
The stderr and stdout is empty, according to galaxy.
here is paster.log output for quikr when i run it.
galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user == "user" quikr -v -k 0 -s /data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # else quikr -v -k 0 -s "/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat".mat.gz -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # end if
that doesn't really seem all that helpful though.
It does help - that command isn't going to work at the shell - try it and see?
The problem is your Cheetah if statement has not been processed, and I think it is as simple as you've used invalid syntax in your <command> tag. I think you need to remove the extra spaces to have:
# if ...
Then it might work?