283
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchCreated page with '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 smo…'
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
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
