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11
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bwa" version="0.7.12">
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4 <repository changeset_revision="dcae4134cd62" name="package_bwa_0_7_12" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="bedtools" version="2.24">
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7 <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="samtools" version="1.2">
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10 <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="R" version="3.1.2">
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13 <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="Perl" version="5.18">
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16 <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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17 </package>
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12
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18 <action type="setup_r_environment">
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19 <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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20 <package name="R" version="3.1.2" />
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21 </repository>
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22 <package>https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz</package>
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23 <package>https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz</package>
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24 <package>https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz</package>
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25 <package>https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz</package>
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26 </action>
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27 <action type="setup_perl_environment">
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28 <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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29 <package name="Perl" version="5.18" />
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30 </repository>
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31 <package>https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz</package>
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32 <package>https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz</package>
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33 <package>https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz</package>
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34 <package>https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz</package>
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35 <package>https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz</package>
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36 </action>
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11
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37 </tool_dependency>
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