README.dev.md

Installation

1. Install virtualenv

   pip3 install virtualenv
   

2. Create and activate virtual environment

   mkdir venv
   cd venv
   virtualenv .
   source ./bin/activate
   

3. Clone current repository and install AltAnalyze3 from there

   git clone https://github.com/SalomonisLab/altanalyze3.git
   cd altanalyze3
   pip3 install -e .
   

4. Test installation

   altanalyze3 --help
   

Note, for proper AltAnalyze functionality, you need to have samtools intalled.

Testing

cd tests
./unit_tests_in_docker.sh
./e2e_tests_in_docker.sh
./cwl_tests_in_docker.sh
./wdl_tests_in_docker.sh