Installation

As Sargasso has a number of dependencies on other Python packages, it is strongly recommended to install in an isolated environment using the virtualenv tool. The virtualenvwrapper tool makes managing multiple virtual environments easier.

Create and work in a virtual environment for Sargasso using the virtualenvwrapper tool:

mkproject sargasso

Then install the latest version of the Sargasso package and its Python package dependencies into the virtual environment by running:

pip install git+https://github.com/statbio/Sargasso.git

Note that the Sargasso pipeline uses the Sambamba alignment processing tool, and either the Bowtie2 read aligner (for reads originating from DNA sequencing), or the short RNA-seq read aligner STAR. These should be installed before using Sargasso (though, for example, only STAR needs to be installed if only RNA-seq data is intended to be processed).

Next: Example usage