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Quickstart

This chapter gives the minimal number of commands required for setting up the pipeline on the BIH cluster.

Note

This describes the setup as a pipeline user. If you want to know about the setup as a pipeline developer, see :ref:`installation`.

Install (Mini)conda

First, install miniconda, e.g., into $HOME/miniconda3.

$ wget -O /tmp/Miniconda3-latest-Linux-x86_64.sh \
    https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3

Note

What is conda/miniconda?

Conda is a Python-based package manager that can also package binary files (such as Bioinformatics software). Miniconda is a minimal Conda installation.

If anything goes wrong with your Miniconda installation, you can always just remove $HOME/miniconda3 and start anew.

Now, make sure it is available in your PATH environment variable.

$ export PATH=$HOME/miniconda3/bin:$PATH

Install Snappy Pipeline

The recommended way of installing the CUBI pipeline is via pip.

Replace the X.Y.Z in the definition of VERSION below with the version you find in the README.rst file of the project on the CUBI GitHub.

$ VERSION=vX.Y.Z
$ pip install git+ssh://[email protected]:bihealth/snappy-pipeline.git@v${VERSION}#egg=snappy_pipeline

Or see README.rst for a more detailed installation guide and the environment setup step.