Installation

metaseq relies on the standard Scientific Python Stack, specifically, NumPy, SciPy, matplotlib, and pandas. It also relies on standard genomics tools like BEDTools, samtools, and others.

Installing each of these prerequisites would be time-consuming and frustrating. However conda combined with the bioconda project makes it easy and straightforward.

Easy installation method

The following assumes you have conda installed. conda is a cross-platform package manager that started on Python but now includes other languages and binaries as well. There are two options for installing conda: the Anaconda Python distribution, which includes the full scientific Python stack, or the smaller, barebones Miniconda.

The commands below work with either Linux or Mac OSX. See managing environments to decide if you want to use the main conda environment or an isolated environment. If you want to use an isolated environment, use create -n my-env-name instead of install in the commands below.

Option 1: Install the metaseq package and Python dependencies

conda install --channel bioconda metaseq

Option 2: Install the metaseq package and Python dependencies, plus BEDTools, samtools, htslib, and the UCSC tools bigWigSummary, bedGraphToBigWig, bedToBigBed, and bigBedToBed. This is a good option if you don’t already maintain separate installations of these tools

conda install --channel bioconda metaseq-all

Windows

It is difficult to do bioinformatics work on Windows. The most convenient option will be to run Linux on your Windows machine (via dual-boot or virtual machine), and follow the Linux instructions above to install metaseq and requirements.