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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R" version="3.2.0">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz</action>
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7 <action type="shell_command">./configure</action>
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8 <action type="shell_command">make</action>
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9 <action type="shell_command">make install</action>
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10 <action type="move_file">
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11 <source>R.3.2.0</source>
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12 <destination>$INSTALL_DIR</destination>
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13 </action>
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14 <action type="set_environment">
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15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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16 </action>
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17 </actions>
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18 </install>
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19 <readme>
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20 R-3.2.0 installed now try edgeR
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21 </readme>
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22 </package>
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23 <package name="limma" version="3.24.12">
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24 <install version="1.0">
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25 <actions>
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26 <action type="setup_r_environment">
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27 <!--repository name="limmatest2" owner="deepakjadmin" toolshed="https://testtoolshed.g2.bx.psu.edu"-->
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28 <package name="R" version="3.2.0" />
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29
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30 <action type="download_by_url">http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.24.15.tar.gz?raw=true</action>
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31 <action type="shell_command">R CMD INSTALL limma_3.24.15.tar.gz</action>
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32 </action>
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33 </actions>
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34 </install>
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35 <readme>
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36 limma_3.24.12 installed now try edgeR
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37 </readme>
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38 </package>
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39
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40 </tool_dependency>
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