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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