Installation

Note

If you are on the BIH cluster, first read Quickstart as this also explains the temporary directory.

Prerequisites

The CUBI pipeline requires Python >=3.7 (e.g., from a Miniconda3 installation).

More recent versions also work but other requirements as Snakemake might make it depend on a more recent Python version.

For cluster execution, you need a Snakemake profile available.

Installing a Release

This is the recommended way if you just want to use the pipeline, simply read Quickstart.

Installing as a Developer

It is highly recommended to have a Miniconda installation for the development as this allows for easily resetting everything. You can of course clone the code anywhere you like.

$ mkdir -p ~/Development/pipeline_dev
$ cd ~/Development/pipeline_dev
$ git clone git@github.com:bihealth/snappy-pipeline.git
$ cd snappy_pipeline
$ pip install -e .
$ pip install -r requirements/dev.txt

It’s also a good idea to install some packages required for testing through conda:

$ conda env update --name root --file environment.yaml

(If you do not do this, please make sure that you have git-lfs in your PATH through other means)

Running the Tests

To run the tests, you need to add the packages in requirements/test.txt.

$ cd ~/Development/pipeline_dev
$ py.test

Running the Style Checks

$ cd ~/Development/pipeline_dev
$ flake8

Developer Documentation

Make sure to also read the “Pipeline Developer Docs” section, starting with Developer’s Introduction.