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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="fastx_toolkit" version="0.0.13">
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4 <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="bowtie" version="0.12.7">
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7 <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
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8 </package>
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9 <set_environment version="1.0">
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10 <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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11 </set_environment>
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12 <!--package name="R" version="3.0.1">
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13 <repository name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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14 </package!-->
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15
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16 <package name="ViennaRNA" version="2.1.8">
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17 <install version="1.0">
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18 <actions>
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19 <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz</action>
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20 <action type="shell_command">./configure --prefix=$INSTALL_DIR </action>
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21 <action type="shell_command">make</action>
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22 <action type="shell_command">make install</action>
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23 <action type="set_environment">
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24 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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25 </action>
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26 </actions>
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27 </install>
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28 </package>
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29 <package name="R" version="3.0.1">
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30 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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31
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32 <install version="1.0">
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33 <actions>
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34 <action type="set_environment_for_install">
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35 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
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36 <package name="R" version="3.0.1" />
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37 </repository>
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38 </action>
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39 <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
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40 <action type="shell_command">echo "export PATH=$PATH" > $INSTALL_DIR/env.sh </action>
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41 <action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action>
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42
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43 </actions>
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44 </install>
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45 </package>
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46
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47 <package name="threads" version="1.96">
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48 <install version="1.0">
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49 <actions>
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50 <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
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51 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
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52 <action type="shell_command">
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53 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
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54 make &&
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55 make install
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56 </action>
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57 <action type="set_environment">
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58 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
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59 </action>
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60 </actions>
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61 </install>
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62 </package>
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63
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64
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65 <package name="Parallel-ForkManager" version="1.06">
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66 <install version="1.0">
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67 <actions>
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68 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
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69 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
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70 <action type="shell_command">
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71 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
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72 make &&
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73 make install
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74 </action>
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75 <action type="set_environment">
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76 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
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77 </action>
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78 </actions>
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79 </install>
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80 </package>
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81
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82 <package name="Boost-Graph" version="1.4_001">
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83 <install version="1.0">
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84 <actions>
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85 <action type="download_by_url">http://www.cpan.org/authors/id/D/DU/DUFFEE/Boost-Graph-1.4_001.tar.gz</action>
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86 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
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87 <action type="shell_command">
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88 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
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89 ls &&
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90 make &&
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91 make install
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92 </action>
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93 <action type="set_environment">
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94 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
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95 </action>
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96 </actions>
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97 </install>
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98 </package>
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99
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100 <package name="SVG" version="2.59">
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101 <install version="1.0">
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102 <actions>
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103 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
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104 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
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105 <action type="shell_command">
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106 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
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107 make &&
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108 make install
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109 </action>
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110 <action type="set_environment">
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111 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
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112 </action>
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113 </actions>
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114 </install>
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115 </package>
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116
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117 <!--package name="parent" version="0.228">
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118 <install version="1.0">
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119 <actions>
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120 <action type="download_by_url">http://www.cpan.org/authors/id/C/CO/CORION/parent-0.228.tar.gz</action>
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121 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
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122 <action type="shell_command">
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123 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
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124 make &&
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125 make install
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126 </action>
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127 <action type="set_environment">
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128 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
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129 </action>
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130 </actions>
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131 </install>
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132 </package-->
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133
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134 </tool_dependency>
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