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0
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="trinityrnaseq" version="2013_08_14">
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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://tools.osdd.jnu.ac.in/ngsap/trinityrnaseq_r20140717.tar.gz</action>
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7 <action type="shell_command">make</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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14 </action>
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15 <action type="set_environment">
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16 <environment_variable name="TRINITY_HOME" action="set_to">$INSTALL_DIR</environment_variable>
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17 </action>
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18 </actions>
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19 </install>
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20 <readme>
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21 </readme>
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22 </package>
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23 <package name="samtools" version="0.1.18">
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24 <install version="1.0">
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25 <actions_group>
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26 <actions os="linux" architecture="i386">
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27 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
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28 <action type="move_directory_files">
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29 <source_directory>.</source_directory>
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30 <destination_directory>$INSTALL_DIR</destination_directory>
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31 </action>
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32 </actions>
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33 <actions os="linux" architecture="x86_64">
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34 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action>
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35 <action type="move_directory_files">
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36 <source_directory>.</source_directory>
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37 <destination_directory>$INSTALL_DIR</destination_directory>
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38 </action>
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39 </actions>
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40 <actions os="darwin" architecture="i386">
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41 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
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42 <action type="move_directory_files">
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43 <source_directory>.</source_directory>
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44 <destination_directory>$INSTALL_DIR</destination_directory>
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45 </action>
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46 </actions>
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47 <actions os="darwin" architecture="x86_64">
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48 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action>
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49 <action type="move_directory_files">
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50 <source_directory>.</source_directory>
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51 <destination_directory>$INSTALL_DIR</destination_directory>
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52 </action>
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53 </actions>
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54 <actions>
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55 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2</action>
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56 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
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57 <action type="shell_command">make</action>
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58 <action type="move_file">
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59 <source>samtools</source>
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60 <destination>$INSTALL_DIR/bin</destination>
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61 </action>
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62 <action type="move_file">
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63 <source>libbam.a</source>
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64 <destination>$INSTALL_DIR/lib</destination>
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65 </action>
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66 <action type="move_directory_files">
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67 <source_directory>.</source_directory>
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68 <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
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69 </action>
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70 </actions>
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71 <action type="set_environment">
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72 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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73 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
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74 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
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75 </action>
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76 </actions_group>
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77 </install>
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78 <readme>
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79 </readme>
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80 </package>
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81 <package name="rsem" version="1.1.17">
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82 <install version="1.0">
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83 <actions>
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84 <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz</action>
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85 <action type="shell_command">make</action>
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86 <action type="make_directory">$INSTALL_DIR/bin/sam</action>
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87 <action type="move_file">
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88 <source>sam/samtools</source>
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89 <destination>$INSTALL_DIR/bin/sam</destination>
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90 </action>
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91 <action type="move_file">
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92 <source>convert-sam-for-rsem</source>
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93 <destination>$INSTALL_DIR/bin</destination>
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94 </action>
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95 <action type="move_file">
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96 <source>extract-transcript-to-gene-map-from-trinity</source>
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97 <destination>$INSTALL_DIR/bin</destination>
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98 </action>
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99 <action type="move_file">
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100 <source>rsem-bam2readdepth</source>
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101 <destination>$INSTALL_DIR/bin</destination>
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102 </action>
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103 <action type="move_file">
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104 <source>rsem-bam2wig</source>
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105 <destination>$INSTALL_DIR/bin</destination>
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106 </action>
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107 <action type="move_file">
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108 <source>rsem-build-read-index</source>
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109 <destination>$INSTALL_DIR/bin</destination>
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110 </action>
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111 <action type="move_file">
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112 <source>rsem-calculate-credibility-intervals</source>
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113 <destination>$INSTALL_DIR/bin</destination>
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114 </action>
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115 <action type="move_file">
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116 <source>rsem-calculate-expression</source>
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117 <destination>$INSTALL_DIR/bin</destination>
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118 </action>
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119 <action type="move_file">
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120 <source>rsem-extract-reference-transcripts</source>
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121 <destination>$INSTALL_DIR/bin</destination>
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122 </action>
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123 <action type="move_file">
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124 <source>rsem-gen-transcript-plots</source>
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125 <destination>$INSTALL_DIR/bin</destination>
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126 </action>
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127 <action type="move_file">
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128 <source>rsem-get-unique</source>
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129 <destination>$INSTALL_DIR/bin</destination>
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130 </action>
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131 <action type="move_file">
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132 <source>rsem-parse-alignments</source>
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133 <destination>$INSTALL_DIR/bin</destination>
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134 </action>
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135 <action type="move_file">
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136 <source>rsem-plot-model</source>
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137 <destination>$INSTALL_DIR/bin</destination>
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138 </action>
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139 <action type="move_file">
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140 <source>rsem-plot-transcript-wiggles</source>
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141 <destination>$INSTALL_DIR/bin</destination>
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142 </action>
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143 <action type="move_file">
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144 <source>rsem-prepare-reference</source>
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145 <destination>$INSTALL_DIR/bin</destination>
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146 </action>
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147 <action type="move_file">
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148 <source>rsem-preref</source>
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149 <destination>$INSTALL_DIR/bin</destination>
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150 </action>
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151 <action type="move_file">
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152 <source>rsem-run-em</source>
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153 <destination>$INSTALL_DIR/bin</destination>
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154 </action>
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155 <action type="move_file">
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156 <source>rsem-run-gibbs</source>
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157 <destination>$INSTALL_DIR/bin</destination>
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158 </action>
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159 <action type="move_file">
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160 <source>rsem-simulate-reads</source>
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161 <destination>$INSTALL_DIR/bin</destination>
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162 </action>
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163 <action type="move_file">
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164 <source>rsem-synthesis-reference-transcripts</source>
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165 <destination>$INSTALL_DIR/bin</destination>
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166 </action>
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167 <action type="move_file">
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168 <source>rsem-tbam2gbam</source>
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169 <destination>$INSTALL_DIR/bin</destination>
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170 </action>
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171 <action type="set_environment">
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172 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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173 </action>
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174 </actions>
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175 </install>
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176 <readme>
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177 </readme>
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178 </package>
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179 <package name="eXpress" version="1.5.1">
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180 <install version="1.0">
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181 <actions_group>
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182 <actions os="linux" architecture="x86_64">
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183 <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-linux_x86_64.tgz</action>
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184 <action type="move_directory_files">
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185 <source_directory>.</source_directory>
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186 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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187 </action>
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188 </actions>
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189 <actions os="darwin" architecture="x86_64">
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190 <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-macosx_x86_64.tgz</action>
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191 <action type="move_directory_files">
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192 <source_directory>.</source_directory>
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193 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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194 </action>
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195 </actions>
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196 <actions>
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197 <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz</action>
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198 <action type="shell_command">cmake src -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL_DIR</action>
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199 <action type="shell_command">make && make install</action>
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200 </actions>
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201 <action type="set_environment">
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202 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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203 </action>
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204 </actions_group>
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205 </install>
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206 <readme></readme>
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207 </package>
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208 <package name="bowtie" version="0.12.7">
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209 <install version="1.0">
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210 <actions_group>
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211 <actions os="linux" architecture="x86_64">
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212 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz</action>
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213 <action type="move_directory_files">
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214 <source_directory>.</source_directory>
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215 <destination_directory>$INSTALL_DIR</destination_directory>
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216 </action>
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217 </actions>
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218 <actions os="darwin" architecture="x86_64">
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219 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bowtie/bowtie-0.12.7-macos-10.5-x86_64.tgz</action>
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220 <action type="move_directory_files">
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221 <source_directory>.</source_directory>
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222 <destination_directory>$INSTALL_DIR</destination_directory>
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223 </action>
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224 </actions>
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225 <actions os="linux" architecture="i386">
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226 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bowtie/bowtie-0.12.7-linux-i386.tgz</action>
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227 <action type="move_directory_files">
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228 <source_directory>.</source_directory>
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229 <destination_directory>$INSTALL_DIR</destination_directory>
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230 </action>
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231 </actions>
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232 <actions os="darwin" architecture="i386">
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233 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/bowtie/bowtie-0.12.7-macos-10.5-i386.tgz</action>
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234 <action type="move_directory_files">
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235 <source_directory>.</source_directory>
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236 <destination_directory>$INSTALL_DIR</destination_directory>
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237 </action>
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238 </actions>
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239 <actions>
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240 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
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241 <action type="shell_command">make</action>
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242 <action type="move_file">
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243 <source>bowtie</source>
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244 <destination>$INSTALL_DIR</destination>
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245 </action>
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246 <action type="move_file">
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247 <source>bowtie-build</source>
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248 <destination>$INSTALL_DIR</destination>
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249 </action>
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250 <action type="move_file">
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251 <source>bowtie-inspect</source>
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252 <destination>$INSTALL_DIR</destination>
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253 </action>
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254 </actions>
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255 <action type="set_environment">
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256 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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257 </action>
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258 </actions_group>
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259 </install>
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260 <readme></readme>
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261 </package>
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262 <package name="bowtie2" version="2.1.0">
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263 <install version="1.0">
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264 <actions_group>
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265 <actions os="linux" architecture="x86_64">
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266 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz</action>
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267 <action type="move_directory_files">
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268 <source_directory>.</source_directory>
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269 <destination_directory>$INSTALL_DIR</destination_directory>
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270 </action>
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271 </actions>
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272 <actions os="darwin" architecture="x86_64">
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273 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bowtie2/bowtie2-2.1.0-macos-x86_64.tgz</action>
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274 <action type="move_directory_files">
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275 <source_directory>.</source_directory>
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276 <destination_directory>$INSTALL_DIR</destination_directory>
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277 </action>
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278 </actions>
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279 <actions os="linux" architecture="i386">
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280 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bowtie2/bowtie2-2.1.0-linux-i386.tgz</action>
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281 <action type="move_directory_files">
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282 <source_directory>.</source_directory>
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283 <destination_directory>$INSTALL_DIR</destination_directory>
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284 </action>
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285 </actions>
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286 <actions os="darwin" architecture="i386">
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287 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/bowtie2/bowtie2-2.1.0-macos-i386.tgz</action>
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288 <action type="move_directory_files">
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289 <source_directory>.</source_directory>
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290 <destination_directory>$INSTALL_DIR</destination_directory>
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291 </action>
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292 </actions>
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293 <actions>
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294 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
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295 <action type="shell_command">make</action>
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296 <action type="move_file">
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297 <source>bowtie2</source>
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298 <destination>$INSTALL_DIR</destination>
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299 </action>
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300 <action type="move_file">
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301 <source>bowtie2-align</source>
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302 <destination>$INSTALL_DIR</destination>
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303 </action>
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304 <action type="move_file">
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305 <source>bowtie2-build</source>
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306 <destination>$INSTALL_DIR</destination>
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307 </action>
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308 <action type="move_file">
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309 <source>bowtie2-inspect</source>
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310 <destination>$INSTALL_DIR</destination>
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311 </action>
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312 </actions>
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313 <action type="set_environment">
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314 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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315 </action>
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316 </actions_group>
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317 </install>
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318 <readme></readme>
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319 </package>
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320 <package name="tophat2" version="2.0.9">
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321 <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tophat2" owner="devteam" changeset_revision="ae06af1118dc" />
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322 </package>
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323 <package name="blast+" version="2.2.29">
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324 <repository toolshed="http://toolshed.g2.bx.psu.edu" name="ncbi_blast_plus" owner="devteam" changeset_revision="2fe07f50a41e" />
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325 </package>
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326 <package name="cufflinks" version="2.1.1">
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327 <repository toolshed="http://toolshed.g2.bx.psu.edu" name="cufflinks" owner="devteam" changeset_revision="9aab29e159a7" />
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328 </package>
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329 <package name="cufflinks" version="2.2.1">
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330 <repository toolshed="http://toolshed.g2.bx.psu.edu" name="cuffmerge" owner="devteam" changeset_revision="b6e3849293b1" />
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331 </package>
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332 </tool_dependency>
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333
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