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Installation
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.
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
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
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.
See Development for details on building a docker container.
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