diff setup-mac.sh @ 10:e904265469af draft

Uploaded setup script for mac

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/setup-mac.sh	Thu Aug 18 18:41:35 2016 -0400
@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+# Homebrew
+ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
+
+# python
+brew install python
+
+# pip
+curl -O http://python-distribute.org/distribute_setup.py
+python distribute_setup.py
+curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
+python get-pip.py
+
+# wget
+brew install wget
+
+# clean after installation
+rm -t tmp
+
+# Install pysam library
+pip install pysam
+
+# Install numpy library
+pip install numpy
+
+# Install Bio Python
+pip install biopython
+
+# install bedtools
+brew install homebrew/science/bedtools
+
+# install ART
+mkdir cnvsim/ART
+wget -O cnvsim/ART/art.tgz http://www.niehs.nih.gov/research/resources/assets/docs/artsrcgreatsmokymountains041716macostgz.tgz
+tar -xvzf cnvsim/ART/art.tgz -C cnvsim/ART
+rm cnvsim/ART/art.tgz
+mv cnvsim/ART/art_src_GreatSmokyMountains_MacOS/art_illumina cnvsim/ART/art_illumina
+rm -rf cnvsim/ART/art_src_GreatSmokyMountains_MacOS
+
+