Installation
This package is not yet on PyPi. These instructions are for manual installation into a virtual environment. DegNorm is only supported on *Nix platforms.
Installing DegNorm in a conda environment
1. Clone the DegNorm repository and cd into it.
git clone https://github.com/NUStatBioinfo/DegNorm.git
cd DegNorm
2. Create a conda virtual environment and activate it:
conda create -n degnorm python=3.6
source activate degnorm
3. Run the install script
./install
Requirements for degnorm_mpi
degnorm_mpi is the distributed implementation of the DegNorm pipeline.
To use degnorm_mpi, the mpi4py package must be installed.
This requires the MPICH MPI library be installed and configured across your computing environment.
From the install script, mpi4py will be installed for you if the mpiexec command is available in your $PATH, indicating that MPI
is available in your computing environment. If you're running DegNorm in a high performance computing environment (e.g. if you're at a university or research institute),
it is most likely the case that MPI is already installed and available to you in the form of an environment module. Just check that the mpiexec and/or
mpirun commands are available to you at the command line when running ./install, and you should be
all set to run the distributed pipeline with degnorm_mpi.
If MPI is not installed in your compute environment, you will need to take additional steps to do so, or contact your system administrator. See MPICH home for details.
Testing
Check the successful installation of degnorm on your machine with the degnorm_test command. This runs all unit tests
and a minimal DegNorm pipeline run on a small batch of sample data. If you have installed the mpi4py package, and
you happen to be testing in a multi-node environment, degnorm_test will also test a small distributed pipeline run with degnorm_mpi.
By default, degnorm_test will clean up after itself by removing the temporary directory containing the output
of a full pipeline test run. If you would like to keep and inspect that directory, add the --keep-output flag:
degnorm_test --keep-output