Yes, it seems that has solved the problem! I knew it was something silly.
thank you all On 12 September 2014 11:37, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison <mutanttur...@gmail.com> > 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 ... > > Not: > > # if ... > > Then it might work? > > Peter >
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