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1 <?xml version="1.0"?>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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2 <tool_dependency>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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3 <package name="R" version="3.1.2">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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4 <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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5 owner="iuc" prior_installation_required="True"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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6 toolshed="http://toolshed.g2.bx.psu.edu" />
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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7 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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8 <package name="readline" version="6.2">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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9 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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10 owner="iuc" prior_installation_required="True"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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11 toolshed="http://toolshed.g2.bx.psu.edu" />
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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12 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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13 <package name="rpy2" version="2.3.10">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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14 <install version="1.0">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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15 <actions>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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16 <action type="download_by_url">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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17 https://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.10.tar.gz
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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18 </action>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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19 <action type="set_environment_for_install">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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20 <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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21 owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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22 <package name="readline" version="6.2" />
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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23 </repository>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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24 <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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25 owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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26 <package name="R" version="3.1.2" />
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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27 </repository>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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28 </action>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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29 <action type="shell_command">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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30 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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31 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &&
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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32 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &&
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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33 python setup.py build --r-home $R_HOME --r-home-lib $R_HOME/lib install --install-lib $INSTALL_DIR/lib/python
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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34 </action>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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35 <action type="set_environment">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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36 <environment_variable action="append_to" name="PYTHONPATH">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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37 $INSTALL_DIR/lib/python
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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38 </environment_variable>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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39 <environment_variable action="append_to" name="LD_LIBRARY_PATH">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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40 $ENV[READLINE_LIB_PATH]
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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41 </environment_variable>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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42 <environment_variable action="append_to" name="LD_LIBRARY_PATH">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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43 $ENV[RHOME]/lib
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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44 </environment_variable>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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45 <environment_variable action="append_to" name="LD_LIBRARY_PATH">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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46 $ENV[R_ROOT_DIR]/lib
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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47 </environment_variable>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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48 </action>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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49 </actions>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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50 </install>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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51 <readme>rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R,
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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52 a proposed high-level interface, including wrappers to graphical libraries,
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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53 as well as R-like structures and functions.
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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54
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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55 http://rpy.sourceforge.net/rpy2.html
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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56 </readme>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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57 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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58 <package name="riboseqr_wrapper_deps" version="0.4.0">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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59 <install version="1.0">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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60 <actions>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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61 <action type="setup_r_environment">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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62 <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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63 owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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64 <package name="R" version="3.1.2" />
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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65 </repository>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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66 <package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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67 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/BiocGenerics_0.12.1.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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68 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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69 <package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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70 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/S4Vectors_0.4.0.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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71 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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72 <package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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73 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/IRanges_2.0.1.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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74 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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75 <package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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76 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/GenomeInfoDb_1.2.5.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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77 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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78 <package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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79 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/XVector_0.6.0.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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80 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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81 <package>
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82 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/GenomicRanges_1.18.4.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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83 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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84 <package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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85 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/abind_1.4-3.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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86 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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87 <package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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88 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/baySeq_2.0.50.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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89 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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90 <package>
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91 https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/riboSeqR_1.0.5.tar.gz?raw=true
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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92 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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93 </action>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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94 </actions>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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95 </install>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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96 <readme>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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97 Dependency installation for riboseqr_wrapper
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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98 </readme>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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99 </package>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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100 </tool_dependency>
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