install_bioconda.md

Installing ngs-bits binaries (Linux/macOS)

Bioconda is a bioinformatics resource that extends the Conda package manager with bioinformatics software packages.
ngs-bits binaries can be easily built using Bioconda.

Setting up Bioconda (if not done yet)

To install ngs-bits binaries, follow these instructions:

1. Install Miniconda, which installs a minimal version of the conda package manager.

2. Add the Bioconda channels using the conda command:

    > conda config --add channels defaults
    > conda config --add channels conda-forge
    > conda config --add channels bioconda
   

Installing ngs-bits

Install the ngs-bits package using conda:

> conda install ngs-bits

Executing

Now the ngs-bits executables are installed into the conda bin folder.
For example, try this:

> bin/ReadQC --help

Adding reference genome to the settings

Some of the ngs-bits tools need a reference genome in FASTA format.
You can set the reference genome on the command line, e.g. the -ref parameter of the VcfLeftNormalize tool.

To avoid having to set the reference genome for each call, you can set up a settings file.
Copy the template:

> cp bin/settings.ini.example bin/settings.ini

and then set the reference_genome parameter in the bin/settings.ini file.