Installation

The auto-process-ngs package is available from its GitHub respository at

• https://github.com/fls-bioinformatics-core/auto_process_ngs

Specific versions can be obtained as tar.gz archives from:

• https://github.com/fls-bioinformatics-core/auto_process_ngs/releases

The software is written in Python (see Supported Python versions for a list of supported versions).

It is recommended to install the package into a Python virtualenv, for example:

virtualenv venv.ap
. venv.ap/bin/activate

To install a specific version, first download and unpack the source code, e.g.:

wget https://github.com/fls-bioinformatics-core/auto_process_ngs/archive/0.10.0.tar.gz
tar zxf 0.10.0.tar.gz

Then install the requirements and then rest of the packages:

pip install -r auto_process_ngs-0.10.0/requirements.txt
pip install ./auto_process_ngs-0.10.0

In addition a number of external software packages are required for the Fastq generation and QC pipelines; these are listed in the requirements documentation.

The installation may also require some configuration to tailor it to the local environment (for example, if running on a compute cluster); this is outlined in more detail in the configuration documentation.