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9
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1 #!/usr/bin/env bash
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2
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3 # python
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4 sudo apt-get install python
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5
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6 # pip
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7 sudo apt-get install python-pip
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8
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9 # wget
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10 sudo apt-get install wget
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11
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12 # Install pysam library
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13 sudo pip install pysam
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14
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15 # Install Bio Python
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16 sudo pip install biopython
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17
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18 # install bedtools
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19 sudo apt-get install bedtools
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20
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21 # install ART
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22 mkdir lib/ART
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23 wget -O cnvsim/ART/art.tgz http://www.niehs.nih.gov/research/resources/assets/docs/artsrcgreatsmokymountains041716linuxtgz.tgz
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24 tar -xvzf cnvsim/ART/art.tgz -C cnvsim/ART
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25 rm cnvsim/ART/art.tgz
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26 mv cnvsim/ART/art_src_GreatSmokyMountains_Linux/art_illumina cnvsim/ART/art_illumina
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27 rm -rf cnvsim/ART/art_src_GreatSmokyMountains_Linux
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