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