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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R_3_0_1" version="3.0.1">
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4 <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="rsem" version="1.2.8">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.8.tar.gz</action>
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10 <action type="shell_command">make</action>
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11 <action type="make_directory">$INSTALL_DIR/bin/sam</action>
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12 <action type="move_file">
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13 <source>sam/samtools</source>
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14 <destination>$INSTALL_DIR/bin/sam</destination>
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15 </action>
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16 <action type="move_file">
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17 <source>convert-sam-for-rsem</source>
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18 <destination>$INSTALL_DIR/bin</destination>
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19 </action>
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20 <action type="move_file">
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21 <source>extract-transcript-to-gene-map-from-trinity</source>
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22 <destination>$INSTALL_DIR/bin</destination>
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23 </action>
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24 <action type="move_file">
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25 <source>rsem-bam2readdepth</source>
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26 <destination>$INSTALL_DIR/bin</destination>
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27 </action>
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28 <action type="move_file">
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29 <source>rsem-bam2wig</source>
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30 <destination>$INSTALL_DIR/bin</destination>
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31 </action>
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32 <action type="move_file">
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33 <source>rsem-build-read-index</source>
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34 <destination>$INSTALL_DIR/bin</destination>
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35 </action>
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36 <action type="move_file">
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37 <source>rsem-calculate-credibility-intervals</source>
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38 <destination>$INSTALL_DIR/bin</destination>
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39 </action>
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40 <action type="move_file">
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41 <source>rsem-calculate-expression</source>
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42 <destination>$INSTALL_DIR/bin</destination>
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43 </action>
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44 <action type="move_file">
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45 <source>rsem-extract-reference-transcripts</source>
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46 <destination>$INSTALL_DIR/bin</destination>
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47 </action>
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48 <action type="move_file">
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49 <source>rsem-gen-transcript-plots</source>
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50 <destination>$INSTALL_DIR/bin</destination>
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51 </action>
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52 <action type="move_file">
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53 <source>rsem-get-unique</source>
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54 <destination>$INSTALL_DIR/bin</destination>
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55 </action>
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56 <action type="move_file">
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57 <source>rsem-parse-alignments</source>
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58 <destination>$INSTALL_DIR/bin</destination>
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59 </action>
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60 <action type="move_file">
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61 <source>rsem-plot-model</source>
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62 <destination>$INSTALL_DIR/bin</destination>
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63 </action>
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64 <action type="move_file">
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65 <source>rsem-plot-transcript-wiggles</source>
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66 <destination>$INSTALL_DIR/bin</destination>
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67 </action>
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68 <action type="move_file">
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69 <source>rsem-prepare-reference</source>
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70 <destination>$INSTALL_DIR/bin</destination>
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71 </action>
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72 <action type="move_file">
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73 <source>rsem-preref</source>
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74 <destination>$INSTALL_DIR/bin</destination>
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75 </action>
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76 <action type="move_file">
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77 <source>rsem-run-em</source>
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78 <destination>$INSTALL_DIR/bin</destination>
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79 </action>
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80 <action type="move_file">
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81 <source>rsem-run-gibbs</source>
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82 <destination>$INSTALL_DIR/bin</destination>
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83 </action>
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84 <action type="move_file">
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85 <source>rsem-simulate-reads</source>
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86 <destination>$INSTALL_DIR/bin</destination>
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87 </action>
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88 <action type="move_file">
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89 <source>rsem-synthesis-reference-transcripts</source>
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90 <destination>$INSTALL_DIR/bin</destination>
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91 </action>
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92 <action type="move_file">
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93 <source>rsem-tbam2gbam</source>
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94 <destination>$INSTALL_DIR/bin</destination>
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95 </action>
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96 <action type="move_file">
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97 <source>rsem-control-fdr</source>
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98 <destination>$INSTALL_DIR/bin</destination>
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99 </action>
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100 <action type="move_file">
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101 <source>rsem-generate-data-matrix</source>
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102 <destination>$INSTALL_DIR/bin</destination>
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103 </action>
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104 <action type="move_file">
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105 <source>rsem-generate-ngvector</source>
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106 <destination>$INSTALL_DIR/bin</destination>
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107 </action>
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108 <action type="move_file">
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109 <source>rsem-run-ebseq</source>
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110 <destination>$INSTALL_DIR/bin</destination>
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111 </action>
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112 <action type="move_file">
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113 <source>rsem-sam-validator</source>
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114 <destination>$INSTALL_DIR/bin</destination>
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115 </action>
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116 <action type="move_file">
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117 <source>rsem-scan-for-paired-end-reads</source>
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118 <destination>$INSTALL_DIR/bin</destination>
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119 </action>
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120 <action type="move_file">
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121 <source>rsem_perl_utils.pm</source>
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122 <destination>$INSTALL_DIR/bin</destination>
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123 </action>
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124 <action type="set_environment_for_install">
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125 <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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126 <package name="R_3_0_1" version="3.0.1" />
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127 </repository>
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128 </action>
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129 <action type="shell_command">make ebseq</action>
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130 <action type="make_directory">$INSTALL_DIR/bin/EBSeq</action>
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131 <action type="move_directory_files">
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132 <source_directory>EBSeq/EBSeq</source_directory>
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133 <destination_directory>$INSTALL_DIR/bin/EBSeq</destination_directory>
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134 </action>
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135 <action type="move_directory_files">
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136 <source_directory>EBSeq/blockmodeling</source_directory>
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137 <destination_directory>$INSTALL_DIR/bin/EBSeq</destination_directory>
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138 </action>
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139 <action type="move_file">
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140 <source>EBSeq/rsem-for-ebseq-find-DE</source>
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141 <destination>$INSTALL_DIR/bin/EBSeq</destination>
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142 </action>
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143 <action type="move_file">
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144 <source>EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info</source>
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145 <destination>$INSTALL_DIR/bin/EBSeq</destination>
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146 </action>
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147 <action type="set_environment">
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148 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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149 </action>
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150 </actions>
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151 </install>
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152 <readme>
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153 RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly
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154 interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores,
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155 variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95X credibility interval estimates for expression levels.
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156 For visualization,It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files
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157 can be visualized by both UCSC Genome browser and Broad InstituteXs Integrative Genomics Viewer (IGV).
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158 Transcript-coordinate files can be visualized by IGV.
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159
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160 http://deweylab.biostat.wisc.edu/rsem/README.html
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161 http://deweylab.biostat.wisc.edu/rsem/
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162 </readme>
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163 </package>
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164 </tool_dependency>
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