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24
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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66
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3 <package name="R" version="3.0.3">
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4 <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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66
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5 </package>
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24
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6
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78
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7 <package name="biocLite_edgeR_limma" version="latest">
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24
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8 <install version="1.0">
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9 <actions>
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10 <action type="set_environment_for_install">
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83
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11 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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12 <package name="R" version="3.0.3" />
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13 </repository>
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14
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24
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15 </action>
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16 <action type="make_directory">$INSTALL_DIR</action>
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17 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action>
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18 <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action>
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19 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action>
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20 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action>
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21 <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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22 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action>
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23 <action type="shell_command">export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action>
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24 </actions>
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25 </install>
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26 <readme>
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27 Installs the latest bioc packages: edgeR & Limma
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24
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28 </readme>
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29 </package>
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30
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31 <!-- instead of using "convert", make use of "gm convert" -->
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32 <package name="graphicsmagick" version="1.3.18">
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33 <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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79
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34 </package>
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35
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36 <package name="design_matrix_creator" version="1.0.0">
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37 <install version="1.0">
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38 <actions>
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87
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39 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/</action>
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79
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40 <action type="chmod">
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41 <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
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42 </action>
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43 <action type="set_environment">
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83
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44 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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45 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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79
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46 </action>
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47 </actions>
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48 </install>
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71
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49 </package>
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24
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50 </tool_dependency>
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