| Previous changeset 9:382e447d750c (2016-08-18) Next changeset 11:b8c966f6e302 (2016-08-18) |
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Commit message:
Uploaded setup script for mac |
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added:
setup-mac.sh |
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| diff -r 382e447d750c -r e904265469af setup-mac.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/setup-mac.sh Thu Aug 18 18:41:35 2016 -0400 |
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| @@ -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 + + |