From 467651c6a33c8878613023cd42fa59f248a0df3c Mon Sep 17 00:00:00 2001 From: Graham McVicker Date: Mon, 25 Apr 2016 19:16:18 -0700 Subject: [PATCH] Update README.md --- README.md | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 10b7c18..937fe98 100644 --- a/README.md +++ b/README.md @@ -59,9 +59,9 @@ The easiest way to install [HDF5](https://www.hdfgroup.org/HDF5/), [numpy](http://www.numpy.org), [scipy](http://scipy.org) and [Pytables](http://www.pytables.org/) is to download and install [Anaconda](http://continuum.io/downloads). *Installing Anaconda is -highly recommended.* After installing Anaconda, the only dependency -that must be downloaded and installed is -[pysam](https://github.com/pysam-developers/pysam). +highly recommended.* After installing Anaconda, configure [Bioconda] (https://bioconda.github.io/) +and do `conda install pysam`, or download and install +[pysam](https://github.com/pysam-developers/pysam) directly. ## Installation @@ -69,7 +69,13 @@ that must be downloaded and installed is 1. Download and install [Anaconda](http://continuum.io/downloads), (or download and install Numpy, Scipy, HDF5, and Pytables separately). -2. Download and install [pysam](https://github.com/pysam-developers/pysam) +2. Configure Bioconda and install pysam: + + conda config --add channels r + conda config --add channels bioconda + conda install pysam + Alternatively, download and install [pysam](https://github.com/pysam-developers/pysam) + yourself. 3. Make sure that the HDF5 library is in your library path. For example on Linux or OSX you can add the following to your .bashrc or .profile (replace