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29
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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=$INSTALL_DIR/lib</action>
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8 <action type="shell_command">make</action>
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9 <action type="move_file">
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10 <source>bin/R</source>
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11 <destination>$INSTALL_DIR/lib/bin</destination>
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12 </action>
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13 <action type="set_environment">
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14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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15 </action>
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16 </actions>
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17 </install>
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18 <readme>
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19 You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.
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20 </readme>
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21 </package>
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22 <package name="samtools" version="0.1.18">
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23 <install version="1.0">
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24 <actions>
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25 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
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26 <action type="shell_command">make</action>
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27 <action type="move_file">
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28 <source>samtools</source>
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29 <destination>$INSTALL_DIR/bin</destination>
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30 </action>
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31 <action type="move_file">
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32 <source>bcftools/bcftools</source>
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33 <destination>$INSTALL_DIR/bin</destination>
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34 </action>
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35 <action type="set_environment">
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36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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37 </action>
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38 </actions>
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39 </install>
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40 <readme>Both BCFTools and Samtools installed in this dependency.Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
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41 </package>
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42 <package name="rseqc" version="2.3.7">
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43 <install version = "1.0">
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44 <actions>
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45 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
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46 <action type="shell_command">python setup.py install --root $INSTALL_DIR/lib/rseqc</action>
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47 <action type="set_environment">
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48 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/lib/python2.7/site-packages
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49 </action>
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50 <action type="set_environment">
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51 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/bin</environment_variable>
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52 </action>
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53 </actions>
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54 </install>
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55 <readme>
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56 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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57 </readme>
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58 </package>
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59
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60 </tool_dependency>
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