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INSTALL.md

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Prerequisites

The following software is currently required if you build from scratch:

  • git
  • CMake >= 3.11
  • A reasonably new C++ compiler
  • Python 3
  • OpenMP for shared memory parallelization (optional)

Building

This sequence of commands lets you start from scratch:

git clone https://github.com/ssciwr/hammingdist.git
cd hammingdist
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make distance
make test

This should (successfully) build the executable distance in the build subdirectory, and run the tests. If cmake picks up the wrong compiler, it can be explicitly enforced by adding -DCMAKE_CXX_COMPILER=<path-to-compiler> to the cmake call (in that case it is best to remove the build directory and start from scratch).

To enable OpenMP multi-threading, add -DHAMMING_WITH_OPENMP=ON to the cmake call.

Running

The tool can be run from the command line:

./distance <path-to-input> <n>

Here, <path-to-input> must point to a fasta dataset, e.g. by putting ../data/example.fasta after putting a data file in the data directory. n is the maximum number of gene sequences that the tool should read. This can be a smaller number than the number of gene sequences in the dataset.

The output is currently written to a file distances.csv. The output is a full matrix, not only the triangular part of the symmetric matrix.

If running in parallel with OpenMP, you can control the number of threads available by changing the environment variable OMP_NUM_THREADS:

OMP_NUM_THREADS=8 ./distance <path-to-input> <n>

Building the Python interface

This sequence of command should build the Python interface:

git clone --recursive https://github.com/ssciwr/hammingdist.git
cd hammingdist

mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make hammingdist

If the wrong version of Python is found, it can be set by adding -DPYTHON_EXECUTABLE=\path\to\python to the cmake command.

Deploying the Python interface

The Python packages are currently built using Github Actions with the project ciwheelbuild. A wheel build and deploy can be triggered by creating a release in Github. Of course, Github Actions should be enabled and the PyPI API access token needs to be stored a secret on the project.