First-time setup

  1. Install conda.

lcdb-workflows depends heavily on the conda package manager to ensure reproducible environments. If you don’t already have conda, install miniconda (Python 3 version recommended).

  1. Clone the repository:

    git clone https://github.com/lcdb/lcdb-workflows.git

3. Run the tests. Set –threads to as many cores as you have on your machine. With 8 cores, this takes about 6 min:

test/run_test.py workflows/mapping/Snakefile --clean --build-env --threads 8

The output will be in workflows/mapping/pasilla.

Subsequent setup

The lcdb/lcdb-init.py script can be used to initialize a working repo in a new working directory.