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 ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/