This package contains several tools for projects and data management in the National Genomics Infrastructure in Stockholm, Sweden.
You can install your own fork of taca in for instance a local conda environment for development. Provided you have conda installed:
# clone the repo
git clone https://github.com/<username>/TACA.git
# create an environment
conda create -n taca_dev python=2.7
conda activate taca_dev
# install TACA and dependencies for developoment
cd TACA
python setup.py develop
pip install -r ./requirements-dev.txt
# Check that tests pass:
cd tests && nosetests -v -s
There is also a plugin for the deliver command. To install this in the same development environment:
# Install taca delivery plugin for development
git clone https://github.com/<username>/TACA.git
cd ../taca-ngi-pipeline
python setup.py develop
pip install -r ./requirements-dev.txt
# add required config files and env for taca delivery plugin
echo "foo:bar" >> ~/.ngipipeline/ngi_config.yaml
mkdir ~/.taca && cp tests/data/taca_test_cfg.yaml ~/.taca/taca.yaml
export CHARON_BASE_URL="http://tracking.database.org"
export CHARON_API_TOKEN="charonapitokengoeshere"
# Check that tests pass:
cd tests && nosetests -v -s
For a more detailed documentation please go to the documentation page.