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4
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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="2.15.1">
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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-2/R-2.15.1.tar.gz</action>
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7 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
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8 <action type="shell_command">make</action>
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9 <action type="set_environment">
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10 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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11 </action>
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12 </actions>
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13 </install>
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14 <readme>You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.</readme>
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15 </package>
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16 <package name="samtools" version="0.1.18">
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17 <install version="1.0">
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18 <actions>
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19 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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20 <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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21 <action type="shell_command">make</action>
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22 <action type="move_file">
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23 <source>samtools</source>
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24 <destination>$INSTALL_DIR/bin</destination>
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25 </action>
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26 <action type="move_file">
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27 <source>misc/maq2sam-long</source>
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28 <destination>$INSTALL_DIR/bin</destination>
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29 </action>
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30 <action type="set_environment">
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31 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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32 </action>
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33 </actions>
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34 </install>
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35 <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
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36 </package>
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37 <package name="rseqc" version="2.3.7">
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38 <install version = "1.0">
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39 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
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40 <action type="shell_command">python setup.py install</action>
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41 <action action="move_directory_files">
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42 <source_directory>.</source_directory>
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43 <destination_directory>$INSTALL_DIR/lib/rseqc</destination_directory>
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44 </action>
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45 <action type="set_environment">
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46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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47 </action>
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48 </actions>
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49 </install>
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50 <readme>
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51 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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52 </readme>
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53 </package>
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54
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55 </tool_dependency>
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