pimentel / bioinformatics_software

Basic bioinformatics tooling

bioinformatics software

Mostly a template for snakemake to download and install software that might be used in the workflow. This is meant to be fairly lightweight so it requires minimal tooling.

Current requirements:

• snakemake
• curl
• basic UNIX utilities

configuration

You MUST define the following 2 variables in config.py:

• BASE: a base destination for files. e.g.: /Users/hjp on Mac or /home/hjp on Linux.
• OS: 'mac' or 'linux' currently supported.

Here is an example config.py:

BASE = '/Users/hjp'
OS = 'mac'

Make sure to change BASE in Snakefile to the destination you would like to install things into.

supported tools

• kallisto 0.43.1
• bowtie2 2.3.2
• cufflinks 2.2.1