We provide a sample package mysub.tgz for the submission.
The file contains a startscript (in bash) mysub, which calls two subscripts (foo and foo2) from the subfolder bin/. The output of foo is linked to the input of foo2 by a pipe. This should provide you with a sample for your standard usecase.
The script only outputs a line that is only solution for the last testcase.
We suggest that you try with the Lite Tracks, which are designed to upload only instances for format testing.