Mercurial > repos > jjohnson > package_rsem_1_2_7
comparison tool_dependencies.xml @ 0:37fc24869870 draft default tip
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| author | jjohnson |
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| date | Fri, 22 Nov 2013 16:27:37 -0500 |
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| -1:000000000000 | 0:37fc24869870 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="rsem" version="1.2.7"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.7.tar.gz</action> | |
| 7 <action type="shell_command">make</action> | |
| 8 | |
| 9 <action type="move_file"> | |
| 10 <source>convert-sam-for-rsem</source> | |
| 11 <destination>$INSTALL_DIR/bin</destination> | |
| 12 </action> | |
| 13 <action type="move_file"> | |
| 14 <source>extract-transcript-to-gene-map-from-trinity</source> | |
| 15 <destination>$INSTALL_DIR/bin</destination> | |
| 16 </action> | |
| 17 <action type="move_file"> | |
| 18 <source>rsem-bam2readdepth</source> | |
| 19 <destination>$INSTALL_DIR/bin</destination> | |
| 20 </action> | |
| 21 <action type="move_file"> | |
| 22 <source>rsem-bam2wig</source> | |
| 23 <destination>$INSTALL_DIR/bin</destination> | |
| 24 </action> | |
| 25 <action type="move_file"> | |
| 26 <source>rsem-build-read-index</source> | |
| 27 <destination>$INSTALL_DIR/bin</destination> | |
| 28 </action> | |
| 29 <action type="move_file"> | |
| 30 <source>rsem-calculate-credibility-intervals</source> | |
| 31 <destination>$INSTALL_DIR/bin</destination> | |
| 32 </action> | |
| 33 <action type="move_file"> | |
| 34 <source>rsem-calculate-expression</source> | |
| 35 <destination>$INSTALL_DIR/bin</destination> | |
| 36 </action> | |
| 37 <action type="move_file"> | |
| 38 <source>rsem-extract-reference-transcripts</source> | |
| 39 <destination>$INSTALL_DIR/bin</destination> | |
| 40 </action> | |
| 41 <action type="move_file"> | |
| 42 <source>rsem-gen-transcript-plots</source> | |
| 43 <destination>$INSTALL_DIR/bin</destination> | |
| 44 </action> | |
| 45 <action type="move_file"> | |
| 46 <source>rsem-get-unique</source> | |
| 47 <destination>$INSTALL_DIR/bin</destination> | |
| 48 </action> | |
| 49 <action type="move_file"> | |
| 50 <source>rsem-parse-alignments</source> | |
| 51 <destination>$INSTALL_DIR/bin</destination> | |
| 52 </action> | |
| 53 <action type="move_file"> | |
| 54 <source>rsem-plot-model</source> | |
| 55 <destination>$INSTALL_DIR/bin</destination> | |
| 56 </action> | |
| 57 <action type="move_file"> | |
| 58 <source>rsem-plot-transcript-wiggles</source> | |
| 59 <destination>$INSTALL_DIR/bin</destination> | |
| 60 </action> | |
| 61 <action type="move_file"> | |
| 62 <source>rsem-prepare-reference</source> | |
| 63 <destination>$INSTALL_DIR/bin</destination> | |
| 64 </action> | |
| 65 <action type="move_file"> | |
| 66 <source>rsem-preref</source> | |
| 67 <destination>$INSTALL_DIR/bin</destination> | |
| 68 </action> | |
| 69 <action type="move_file"> | |
| 70 <source>rsem-run-em</source> | |
| 71 <destination>$INSTALL_DIR/bin</destination> | |
| 72 </action> | |
| 73 <action type="move_file"> | |
| 74 <source>rsem-run-gibbs</source> | |
| 75 <destination>$INSTALL_DIR/bin</destination> | |
| 76 </action> | |
| 77 <action type="move_file"> | |
| 78 <source>rsem-simulate-reads</source> | |
| 79 <destination>$INSTALL_DIR/bin</destination> | |
| 80 </action> | |
| 81 <action type="move_file"> | |
| 82 <source>rsem-synthesis-reference-transcripts</source> | |
| 83 <destination>$INSTALL_DIR/bin</destination> | |
| 84 </action> | |
| 85 <action type="move_file"> | |
| 86 <source>rsem-tbam2gbam</source> | |
| 87 <destination>$INSTALL_DIR/bin</destination> | |
| 88 </action> | |
| 89 <action type="move_file"> | |
| 90 <source>rsem-control-fdr</source> | |
| 91 <destination>$INSTALL_DIR/bin</destination> | |
| 92 </action> | |
| 93 <action type="move_file"> | |
| 94 <source>rsem-generate-data-matrix</source> | |
| 95 <destination>$INSTALL_DIR/bin</destination> | |
| 96 </action> | |
| 97 <action type="move_file"> | |
| 98 <source>rsem-generate-ngvector</source> | |
| 99 <destination>$INSTALL_DIR/bin</destination> | |
| 100 </action> | |
| 101 <action type="move_file"> | |
| 102 <source>rsem-run-ebseq</source> | |
| 103 <destination>$INSTALL_DIR/bin</destination> | |
| 104 </action> | |
| 105 <action type="move_file"> | |
| 106 <source>rsem-sam-validator</source> | |
| 107 <destination>$INSTALL_DIR/bin</destination> | |
| 108 </action> | |
| 109 <action type="move_file"> | |
| 110 <source>rsem-scan-for-paired-end-reads</source> | |
| 111 <destination>$INSTALL_DIR/bin</destination> | |
| 112 </action> | |
| 113 <action type="move_file"> | |
| 114 <source>rsem_perl_utils.pm</source> | |
| 115 <destination>$INSTALL_DIR/bin</destination> | |
| 116 </action> | |
| 117 <action type="set_environment"> | |
| 118 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 119 </action> | |
| 120 </actions> | |
| 121 </install> | |
| 122 <readme> | |
| 123 RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly | |
| 124 interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, | |
| 125 variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95X credibility interval estimates for expression levels. | |
| 126 For visualization,It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files | |
| 127 can be visualized by both UCSC Genome browser and Broad InstituteXs Integrative Genomics Viewer (IGV). | |
| 128 Transcript-coordinate files can be visualized by IGV. | |
| 129 | |
| 130 http://deweylab.biostat.wisc.edu/rsem/README.html | |
| 131 http://deweylab.biostat.wisc.edu/rsem/ | |
| 132 </readme> | |
| 133 </package> | |
| 134 </tool_dependency> |