Looks like I found my answer in the user guide ;( Does anyone know the non easy way or is the answer to write a hook for this?
2.3.4 Submitting Jobs by Specifying Executable on Command Line
You can run a PBS job by specifying an executable and its arguments instead of a job script. When you run qsub this way, it runs the executable directly. It does not start a shell, so no shell initialization scripts are run, and execution paths and other environment variables are not set. There is not an easy way to run your command in a different directory. You should make sure that environment variables are set correctly, and you will usually have to specify the full path to the command.
To submit a job directly, you specify the executable on the command line:
For example, to run myprog with the arguments a and b:
To run myprog with the arguments a and b, naming the job JobA,
To use environment variables you define earlier: qsub [] – [] qsub – myprog a b qsub -N JobA – myprog a b
export INFILE=/tmp/myinfile export INDATA=/tmp/mydata qsub – a.out $INFILE $INDATA