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25
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="r3" version="3.0.1">
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4 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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5 </package>package_ghostscript_9_07
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6 <package name="ghostscript" version="9.07">
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7 <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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8 </package>
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9 <package name="graphicsmagick" version="1.3.18">
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10 <repository changeset_revision="50d546dfd6b9" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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11 </package>
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12 <package name="biocbasics" version="2.12">
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13 <install version="1.0">
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14 <actions>
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15 <action type="set_environment_for_install">
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16 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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17 <package name="r3" version="3.0.1" />
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18 </repository>
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19 </action>
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20 <action type="make_directory">$INSTALL_DIR</action>
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21 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action>
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22 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action>
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23 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action>
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24 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action>
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25 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action>
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26 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action>
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27 <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action>
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28 </actions>
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29 </install>
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30 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
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31 It's clunky but this is the most convenient way I could get anything installed into the package_r3
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32 Note we use cran at fred hutch since no fastest mirror thingy
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33 </readme>
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34 </package>
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35 </tool_dependency>
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