Installation
This section describes different ways to install pyANI-plus on the most common operating systems such as Unix/Linux and macOS.
Currently, we support three ways to install pyANI-plus on your system:
- Installation from source (i.e. download/clone from GitHub)
- Installation with Miniconda/Anaconda/Bioconda
- Installation via
pip/PyPI
Installation from source
To install pyANI-plus from source, you can either download it from the Releases page or clone the repository using git.
To get the latest version with git, run the following command in a terminal:
git clone https://github.com/pyani-plus/pyani-plusAlternatively you can visit the Release page and click on one of the avaliable versions to get the source code in compressed form.
Once the download is complete (and uncompressed, if required), navigate to the repository:
cd pyani-plusThen install pyANI-plus by running the appropriate script for your operating system:
make install_linux # For Linux
make install_macos # For macOSInstallation with Miniconda/Anaconda/Bioconda
With a working Miniconda/Anacodna installation that has Bioconda available, install using the command
conda install pyani-plusInstallation via pip/PyPI
Pyani-plus can be installed using the command
pip install pyani-plusCheck the installation
To check if the installation was sucessful, run the following command:
pyani-plus --helpIf the installation was completed correctly, this should display a list of available commands and options, similar to this:
% pyani-plus -h
Usage: pyani-plus [OPTIONS] COMMAND [ARGS]...
╭─ Options ──────────────────────────────────────────────────────────────────────────────╮
│ --version -v Show tool version (on stdout) and quit. │
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy it or │
│ customize the installation. │
│ --help -h Show this message and exit. │
╰────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ─────────────────────────────────────────────────────────────────────────────╮
│ resume Resume any (partial) run already logged in the database. │
│ list-runs List the runs defined in a given pyANI-plus SQLite3 database. │
│ delete-run Delete any single run from the given pyANI-plus SQLite3 database. │
│ export-run Export any single run from the given pyANI-plus SQLite3 database. │
│ plot-run Plot heatmaps and distributions for any single run. │
│ plot-run-comp Plot comparisons between multiple runs. │
│ classify Classify genomes into clusters based on ANI results. │
╰────────────────────────────────────────────────────────────────────────────────────────╯
╭─ ANI methods ──────────────────────────────────────────────────────────────────────────╮
│ anim Execute ANIm calculations, logged to a pyANI-plus SQLite3 │
│ database. │
│ dnadiff Execute mumer-based dnadiff calculations, logged to a pyANI-plus │
│ SQLite3 database. │
│ anib Execute ANIb calculations, logged to a pyANI-plus SQLite3 │
│ database. │
│ fastani Execute fastANI calculations, logged to a pyANI-plus SQLite3 │
│ database. │
│ sourmash Execute sourmash-plugin-branchwater ANI calculations, logged to a │
│ pyANI-plus SQLite3 database. │
│ external-alignment Compute pairwise ANI from given multiple-sequence-alignment (MSA) │
│ file. │
╰────────────────────────────────────────────────────────────────────────────────────────╯