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comparison setup-mac.sh @ 10:e904265469af draft

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Uploaded setup script for mac
author ahosny
date Thu, 18 Aug 2016 18:41:35 -0400
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children 302eb5118a36
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9:382e447d750c 10:e904265469af
1 #!/usr/bin/env bash
2
3 # Homebrew
4 ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
5
6 # python
7 brew install python
8
9 # pip
10 curl -O http://python-distribute.org/distribute_setup.py
11 python distribute_setup.py
12 curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
13 python get-pip.py
14
15 # wget
16 brew install wget
17
18 # clean after installation
19 rm -t tmp
20
21 # Install pysam library
22 pip install pysam
23
24 # Install numpy library
25 pip install numpy
26
27 # Install Bio Python
28 pip install biopython
29
30 # install bedtools
31 brew install homebrew/science/bedtools
32
33 # install ART
34 mkdir cnvsim/ART
35 wget -O cnvsim/ART/art.tgz http://www.niehs.nih.gov/research/resources/assets/docs/artsrcgreatsmokymountains041716macostgz.tgz
36 tar -xvzf cnvsim/ART/art.tgz -C cnvsim/ART
37 rm cnvsim/ART/art.tgz
38 mv cnvsim/ART/art_src_GreatSmokyMountains_MacOS/art_illumina cnvsim/ART/art_illumina
39 rm -rf cnvsim/ART/art_src_GreatSmokyMountains_MacOS
40
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