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Installation

Adam English edited this page Apr 20, 2024 · 10 revisions

Recommended

For stable versions of Truvari, use pip

python3 -m pip install truvari

Specific versions can be installed via

python3 -m pip install truvari==3.2.0

See pypi for a history of all distributed releases.

Manual Installation

To build Truvari directly, clone the repository and switch to a specific tag.

git clone https://github.com/ACEnglish/truvari.git
git checkout tags/v3.0.0
python3 -m pip install .

To see a list of all available tags, run:

git tag -l

If you have an older clone of the repository and don't see the version you're looking for in tags, make sure to pull the latest changes:

git pull
git fetch --all --tags

Mamba / Conda

NOTE!! There is a very old version of Truvari on bioconda that - for unknown reasons - supersedes the newer, supported versions. Users may need to specify to conda which release to build. See this ticket for details.

Truvari releases are automatically deployed to bioconda. Users can follow instructions here (https://mamba.readthedocs.io/en/latest/installation.html) to install mamba. (A faster alternative conda compatible package manager.)

Creating an environment with Truvari and its dependencies.

mamba create -c conda-forge -c bioconda -n truvari truvari

Alternatively, see the conda page for details

conda install -c bioconda truvari

Building from develop

The default branch is develop, which holds in-development changes. This is for developers or those wishing to try experimental features and is not recommended for production. Development is versioned higher than the most recent stable release with an added suffix (e.g. Current stable release is 3.0.0, develop holds 3.1.0-dev). If you'd like to install develop, repeat the steps above but without git checkout tags/v3.0.0. See wiki for details on how branching is handled.

Docker

See Development for details on building a docker container.

edlib error

Some environments have a hard time installing edlib due to a possible cython bug (source). If you seen an error such as the following:

edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory
     198 |  #include "longintrepr.h"

One method to prevent the error message is to run the following commands (source)

python3 -m venv my_env
source my_env/bin/activate
python3 -m pip install --no-cache-dir cython setuptools wheel
EDLIB_USE_CYTHON=1 python3 -m pip install truvari --no-cache
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