Testing the Installation
We recommend that at least the first time, you install the test packages so you can conveniently test the installation and make sure everything runs smoothly. The tests run within a few minutes and are self checking, so unless you see obvious errors, you can be reasonably sure everything is set up properly. You only need to do this once, unless you have made signifcant changes to your Unix system.
sudo dpkg -i debs/biopipe-test*_amd64.deb Unpacking biopipe-testalign (from .../biopipe-testalign_M.n_amd64.deb) ... Selecting previously deselected package biopipe-testumake. Unpacking biopipe-testumake (from .../biopipe-testumake_M.n_amd64.deb) ... Setting up biopipe-testalign (M.n) ... To test the pipeline, run: /usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign This will remove the contents of ~/testalign and then run the aligner test case. The output is verified so you know if anything failed or not. Setting up biopipe-testumake (M.n) ... To test umake, run: /usr/local/biopipe/bin/umake.pl --test ~/testumake This will remove the contents of ~/testumake and then run the umake test case. The output is verified so you know if anything failed or not.
Login as a normal user (not as root) and do:
# Test the aligner (fast, about 3 minutes) /usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign rm -rf ~/testalign # If no error # Test umake (longer, about 15 minutes) /usr/local/biopipe/bin/umake.pl --test ~/testumake rm -rf ~/testumake # If no error