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annotate tool_dependencies.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents b5d2f575ccb6
children 580ee0c4bc4e
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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="2.11.0">
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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.rstudio.com/src/base/R-2/R-2.11.0.tar.gz</action>
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7 <action type="shell_command">
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8 ./configure --enable-R-shlib \
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9 --with-readline=no \
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10 --with-x=no \
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11 --prefix=$INSTALL_DIR \
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12 --libdir=$INSTALL_DIR/lib \
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13 --disable-R-framework
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14 </action>
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15 <action type="shell_command">make &amp;&amp; make install</action>
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16 <action type="set_environment">
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17 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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18 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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19 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
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20 </action>
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21 </actions>
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22 </install>
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23 <readme>
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24 R is a free software environment for statistical computing and graphics.
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25 NOTE: See custom compilation options above
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26 </readme>
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27 </package>
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28 <package name="numpy" version="1.7.1">
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29 <repository toolshed="http://toolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="iuc" changeset_revision="74c21f9bdc39" />
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30 </package>
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31 <package name="rseqc" version="2.3.7">
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32 <install version = "1.0">
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33 <actions>
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34 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
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35 <action type="shell_command">python setup.py install --root $INSTALL_DIR --prefix . --install-lib lib</action>
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36 <action type="set_environment">
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37 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
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38 </action>
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39 <action type="set_environment">
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40 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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41 </action>
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42 </actions>
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43 </install>
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44 <readme>
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45 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
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46 Requires gcc, python, numpy, and R
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47 </readme>
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48 </package>
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49
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50 </tool_dependency>