Installation¶
Using wheels (recommended)¶
The vpsearch package is available from the Python Package Index (PyPI) and can be installed using pip as follows:
python -m pip install vpsearch
On supported platforms (Linux, Intel macOS), this will install a binary wheel that includes the Parasail dependency. On other platforms, vpsearch can be installed from source, and instructions on how to do so can be found below.
Users of Apple Silicon should compile the package from scratch using the instructions below. Note that vpsearch depends on Parasail, a library for fast alignment using Intel-specific SIMD instruction sets. These are not supported on Apple Silicon and even though vpsearch can be made to run on this platform, it will be slow.
Using Docker¶
It is possible to build a Docker image that contains vpsearch as well as all of its dependencies. This is useful, for example, when integrating vpsearch into a workflow manager, like Snakemake, CWL, or WDL.
To build the image, run the following command from the root of this repository:
docker build . -t vpsearch-image
Once the image has been built, vpsearch can then be run from within a
container. Assuming you have a FASTA file of target sequences in the file
database.fasta in the current directory, run the following to build a
vpsearch index:
docker run -it -v $PWD:/data -t vpsearch-image vpsearch build /data/database.fasta
To query the index for a given FASTA file query.fasta of query sequences, run:
docker run -it -v $PWD:/data -t vpsearch-image vpsearch query /data/database.db /data/query.fasta
From source (development environment)¶
For platforms where no binary wheel is available, or in order to contribute to the codebase, it is necessary to install the package from source. To do so, you will need a C and C++ compiler with support for the AVX2 and AVX512 instruction sets (on Linux, version 4.9.2 and up of the gcc/g++ compiler will do, while on macOS any recent version of clang is sufficient).
Using pip, the package can be installed in development mode in your Python environment in the normal way:
python -m pip install -e .
To verify that everything works as expected, you can run the unit test suite via:
python -m unittest discover -v vpsearch
