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61
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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76
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3 <package name="ghostscript" version="9.07">
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4 <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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61
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5 </package>
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6 <package name="graphicsmagick" version="1.3.18">
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7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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8 </package>
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91
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9 <package name="r303" version="3.0.3">
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10 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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11 </package>
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61
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12 <package name="biocbasics" version="2.14">
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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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91
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16 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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87
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17 <package name="r303" version="3.0.3" />
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61
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18 </repository>
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19 </action>
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102
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20 <action type="make_directory">$INSTALL_DIR</action>
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21 <action type="shell_command">echo 'bioclite = "http://bioconductor.org/biocLite.R"' > $INSTALL_DIR/runme.R</action>
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22 <action type="shell_command">echo "source(bioclite)" >> $INSTALL_DIR/runme.R</action>
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23 <action type="shell_command">echo 'installme=c("edgeR","limma","DESeq","DESeq2")' >> $INSTALL_DIR/runme.R</action>
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24 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action>
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25 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action>
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26 <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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27 <action type="shell_command">echo 'quit(save="no")' >> $INSTALL_DIR/runme.R</action>
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28 <action type="shell_command">echo "PATH=$PATH 1>&2"</action>
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29 <action type="shell_command">echo "R_PATH=$R_PATH 1>&2"</action>
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30 <action type="shell_command">export PATH=$PATH && $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action>
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61
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31 </actions>
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32 </install>
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33 <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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34 It's clunky but this is the most convenient way I could get anything installed into the package_r3
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35 Note we use cran at fred hutch since no fastest mirror thingy
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36 If atlas will not compile - eg: it thinks autoscaling is on or something,
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37 you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references
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38 </readme>
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39 </package>
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40 </tool_dependency>
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