# HG changeset patch
# User ahosny
# Date 1471560069 14400
# Node ID 382e447d750cffb87c991d79602b921d97aefe3e
# Parent  31047e84cc0d1173bf963ee38f6cc0d869a408f6
Uploaded setup script for linux

diff -r 31047e84cc0d -r 382e447d750c setup-linux.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/setup-linux.sh	Thu Aug 18 18:41:09 2016 -0400
@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+
+# python
+sudo apt-get install python
+
+# pip
+sudo apt-get install python-pip
+
+# wget
+sudo apt-get install wget
+
+# Install pysam library
+sudo pip install pysam
+
+# Install numpy library
+sudo pip install numpy
+
+# Install Bio Python
+sudo pip install biopython
+
+# install bedtools
+sudo apt-get install bedtools
+
+# install ART
+mkdir lib/ART
+wget -O cnvsim/ART/art.tgz http://www.niehs.nih.gov/research/resources/assets/docs/artsrcgreatsmokymountains041716linuxtgz.tgz
+tar -xvzf cnvsim/ART/art.tgz -C cnvsim/ART
+rm cnvsim/ART/art.tgz
+mv cnvsim/ART/art_src_GreatSmokyMountains_Linux/art_illumina cnvsim/ART/art_illumina
+rm -rf cnvsim/ART/art_src_GreatSmokyMountains_Linux