Installing Seal

To begin, Seal needs to know where to find the HadoopBAM jars (if you don’t have it yet, see the Installation - Dependencies page before continuing). To tell it, set the environment variable HADOOP_BAM to point to the root HadoopBAM path:

export HADOOP_BAM=/home/me/hadoop-bam

Then follow the typical procedure for building Python programs:

python setup.py build
python setup.py install

The above will install to the current system’s /usr/local/, which is probably not what you want unless you’re testing on a single-node installation (see Installation - Deploying). To specify a different installation directory try

python setup.py install --user

to install to $HOME/.local/ or

python setup.py install --home <PATH>

to choose a specific installation path.

Creating the documentation

You can find the documentation for the latest Seal release at http://biodoop-seal.sourceforge.net/.

If however you want to build yourself a local copy, you can do so by installing Sphinx, going to the Seal directory and running

python setup.py build_docs

You’ll find the documentation in HTML in docs/_build/html/index.html.

Running unit tests

From the Seal source directory, after having built Seal, you can run the unit tests with the following commands:

PYTHONPATH=`ls -d $(pwd)/build/lib*` python setup.py run_unit_tests

The expression assigned to PYTHONPATH tries to find the lib or lib.linux... subdirectory created by the build process under build. If it doesn’t work, just look it up and insert the value manually; e.g.,

18:40 [pireddu@slynx seal.git] pwd
/u/pireddu/Projects/seal.git
18:40 [pireddu@slynx seal.git] ls build
lib.linux-x86_64-2.7  scripts-2.7
18:40 [pireddu@slynx seal.git] export PYTHONPATH=/u/pireddu/Projects/seal.git/build/lib.linux-x86_64-2.7/
18:40 [pireddu@slynx seal.git] python setup.py run_unit_tests

Running integration tests

Seal also includes a number of integration tests that actually run the applications on known input and verify that the output is as expected. To run these tests you must have correctly installed Seal and your Hadoop must be running and accessible. In fact, running these is a good way to ensure your whole system is working properly.

To run the integration tests try:

python setup.py run_integration_tests