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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bowtie" version="0.12.7">
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4 <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="samtools" version="0.1.18">
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7 <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="pysam" version="0.7.7">
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10 <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="R" version="3.0.3">
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13 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="biocbasics" version="2.14">
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16 <install version="1.0">
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17 <actions>
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18 <action type="set_environment_for_install">
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19 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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20 <package name="R" version="3.0.3" />
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21 </repository>
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22 </action>
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23 <action type="make_directory">$INSTALL_DIR</action>
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24 <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" > $INSTALL_DIR/runme.R</action>
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25 <action type="shell_command">echo "source(bioclite)" >> $INSTALL_DIR/runme.R</action>
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26 <action type="shell_command">echo "installme=c(\"lattice\",\"latticeExtra\")" >> $INSTALL_DIR/runme.R</action>
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27 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action>
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28 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action>
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29 <action type="shell_command">echo "install.packages(c(\"gridBase\",\"gridExtra\"),dependencies=T,repos=\"http://cran.us.r-project.org\")" >> $INSTALL_DIR/runme.R</action>
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30 <action type="shell_command">echo "quit(save=\"no\")" >> $INSTALL_DIR/runme.R</action>
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31 <action type="shell_command">export PATH=$PATH && R CMD BATCH $INSTALL_DIR/runme.R </action>
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32 </actions>
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33 </install>
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34 <readme>Installs some basic bioc packages for the lattice wrapper and grid + gridExtra for managing lattice panels
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35 It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
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36 Note we use cran at fred hutch since no fastest mirror thingy
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37 </readme>
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38 </package>
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39 </tool_dependency>
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