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comparison tool_dependencies.xml @ 0:37fc24869870 draft default tip

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author jjohnson
date Fri, 22 Nov 2013 16:27:37 -0500
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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>