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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="rsem" version="1.2.7">
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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://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.7.tar.gz</action>
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7 <action type="shell_command">make</action>
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8
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9 <action type="move_file">
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10 <source>convert-sam-for-rsem</source>
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11 <destination>$INSTALL_DIR/bin</destination>
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12 </action>
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13 <action type="move_file">
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14 <source>extract-transcript-to-gene-map-from-trinity</source>
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15 <destination>$INSTALL_DIR/bin</destination>
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16 </action>
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17 <action type="move_file">
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18 <source>rsem-bam2readdepth</source>
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19 <destination>$INSTALL_DIR/bin</destination>
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20 </action>
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21 <action type="move_file">
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22 <source>rsem-bam2wig</source>
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23 <destination>$INSTALL_DIR/bin</destination>
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24 </action>
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25 <action type="move_file">
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26 <source>rsem-build-read-index</source>
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27 <destination>$INSTALL_DIR/bin</destination>
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28 </action>
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29 <action type="move_file">
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30 <source>rsem-calculate-credibility-intervals</source>
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31 <destination>$INSTALL_DIR/bin</destination>
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32 </action>
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33 <action type="move_file">
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34 <source>rsem-calculate-expression</source>
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35 <destination>$INSTALL_DIR/bin</destination>
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36 </action>
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37 <action type="move_file">
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38 <source>rsem-extract-reference-transcripts</source>
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39 <destination>$INSTALL_DIR/bin</destination>
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40 </action>
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41 <action type="move_file">
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42 <source>rsem-gen-transcript-plots</source>
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43 <destination>$INSTALL_DIR/bin</destination>
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44 </action>
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45 <action type="move_file">
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46 <source>rsem-get-unique</source>
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47 <destination>$INSTALL_DIR/bin</destination>
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48 </action>
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49 <action type="move_file">
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50 <source>rsem-parse-alignments</source>
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51 <destination>$INSTALL_DIR/bin</destination>
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52 </action>
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53 <action type="move_file">
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54 <source>rsem-plot-model</source>
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55 <destination>$INSTALL_DIR/bin</destination>
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56 </action>
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57 <action type="move_file">
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58 <source>rsem-plot-transcript-wiggles</source>
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59 <destination>$INSTALL_DIR/bin</destination>
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60 </action>
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61 <action type="move_file">
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62 <source>rsem-prepare-reference</source>
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63 <destination>$INSTALL_DIR/bin</destination>
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64 </action>
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65 <action type="move_file">
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66 <source>rsem-preref</source>
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67 <destination>$INSTALL_DIR/bin</destination>
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68 </action>
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69 <action type="move_file">
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70 <source>rsem-run-em</source>
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71 <destination>$INSTALL_DIR/bin</destination>
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72 </action>
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73 <action type="move_file">
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74 <source>rsem-run-gibbs</source>
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75 <destination>$INSTALL_DIR/bin</destination>
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76 </action>
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77 <action type="move_file">
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78 <source>rsem-simulate-reads</source>
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79 <destination>$INSTALL_DIR/bin</destination>
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80 </action>
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81 <action type="move_file">
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82 <source>rsem-synthesis-reference-transcripts</source>
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83 <destination>$INSTALL_DIR/bin</destination>
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84 </action>
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85 <action type="move_file">
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86 <source>rsem-tbam2gbam</source>
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87 <destination>$INSTALL_DIR/bin</destination>
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88 </action>
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89 <action type="move_file">
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90 <source>rsem-control-fdr</source>
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91 <destination>$INSTALL_DIR/bin</destination>
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92 </action>
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93 <action type="move_file">
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94 <source>rsem-generate-data-matrix</source>
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95 <destination>$INSTALL_DIR/bin</destination>
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96 </action>
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97 <action type="move_file">
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98 <source>rsem-generate-ngvector</source>
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99 <destination>$INSTALL_DIR/bin</destination>
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100 </action>
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101 <action type="move_file">
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102 <source>rsem-run-ebseq</source>
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103 <destination>$INSTALL_DIR/bin</destination>
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104 </action>
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105 <action type="move_file">
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106 <source>rsem-sam-validator</source>
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107 <destination>$INSTALL_DIR/bin</destination>
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108 </action>
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109 <action type="move_file">
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110 <source>rsem-scan-for-paired-end-reads</source>
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111 <destination>$INSTALL_DIR/bin</destination>
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112 </action>
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113 <action type="move_file">
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114 <source>rsem_perl_utils.pm</source>
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115 <destination>$INSTALL_DIR/bin</destination>
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116 </action>
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117 <action type="set_environment">
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118 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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119 </action>
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120 </actions>
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121 </install>
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122 <readme>
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123 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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124 interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores,
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125 variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95X credibility interval estimates for expression levels.
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126 For visualization,It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files
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127 can be visualized by both UCSC Genome browser and Broad InstituteXs Integrative Genomics Viewer (IGV).
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128 Transcript-coordinate files can be visualized by IGV.
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129
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130 http://deweylab.biostat.wisc.edu/rsem/README.html
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131 http://deweylab.biostat.wisc.edu/rsem/
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132 </readme>
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133 </package>
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134 </tool_dependency>
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