Mercurial > repos > jjohnson > package_rsem_1_2_8

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author jjohnson
date Fri, 13 Dec 2013 10:12:16 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="R_3_0_1" version="3.0.1">
4 <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="rsem" version="1.2.8">
7 <install version="1.0">
8 <actions>
9 <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.8.tar.gz</action>
10 <action type="shell_command">make</action>
11 <action type="make_directory">$INSTALL_DIR/bin/sam</action>
12 <action type="move_file">
13 <source>sam/samtools</source>
14 <destination>$INSTALL_DIR/bin/sam</destination>
15 </action>
16 <action type="move_file">
17 <source>convert-sam-for-rsem</source>
18 <destination>$INSTALL_DIR/bin</destination>
19 </action>
20 <action type="move_file">
21 <source>extract-transcript-to-gene-map-from-trinity</source>
22 <destination>$INSTALL_DIR/bin</destination>
23 </action>
24 <action type="move_file">
25 <source>rsem-bam2readdepth</source>
26 <destination>$INSTALL_DIR/bin</destination>
27 </action>
28 <action type="move_file">
29 <source>rsem-bam2wig</source>
30 <destination>$INSTALL_DIR/bin</destination>
31 </action>
32 <action type="move_file">
33 <source>rsem-build-read-index</source>
34 <destination>$INSTALL_DIR/bin</destination>
35 </action>
36 <action type="move_file">
37 <source>rsem-calculate-credibility-intervals</source>
38 <destination>$INSTALL_DIR/bin</destination>
39 </action>
40 <action type="move_file">
41 <source>rsem-calculate-expression</source>
42 <destination>$INSTALL_DIR/bin</destination>
43 </action>
44 <action type="move_file">
45 <source>rsem-extract-reference-transcripts</source>
46 <destination>$INSTALL_DIR/bin</destination>
47 </action>
48 <action type="move_file">
49 <source>rsem-gen-transcript-plots</source>
50 <destination>$INSTALL_DIR/bin</destination>
51 </action>
52 <action type="move_file">
53 <source>rsem-get-unique</source>
54 <destination>$INSTALL_DIR/bin</destination>
55 </action>
56 <action type="move_file">
57 <source>rsem-parse-alignments</source>
58 <destination>$INSTALL_DIR/bin</destination>
59 </action>
60 <action type="move_file">
61 <source>rsem-plot-model</source>
62 <destination>$INSTALL_DIR/bin</destination>
63 </action>
64 <action type="move_file">
65 <source>rsem-plot-transcript-wiggles</source>
66 <destination>$INSTALL_DIR/bin</destination>
67 </action>
68 <action type="move_file">
69 <source>rsem-prepare-reference</source>
70 <destination>$INSTALL_DIR/bin</destination>
71 </action>
72 <action type="move_file">
73 <source>rsem-preref</source>
74 <destination>$INSTALL_DIR/bin</destination>
75 </action>
76 <action type="move_file">
77 <source>rsem-run-em</source>
78 <destination>$INSTALL_DIR/bin</destination>
79 </action>
80 <action type="move_file">
81 <source>rsem-run-gibbs</source>
82 <destination>$INSTALL_DIR/bin</destination>
83 </action>
84 <action type="move_file">
85 <source>rsem-simulate-reads</source>
86 <destination>$INSTALL_DIR/bin</destination>
87 </action>
88 <action type="move_file">
89 <source>rsem-synthesis-reference-transcripts</source>
90 <destination>$INSTALL_DIR/bin</destination>
91 </action>
92 <action type="move_file">
93 <source>rsem-tbam2gbam</source>
94 <destination>$INSTALL_DIR/bin</destination>
95 </action>
96 <action type="move_file">
97 <source>rsem-control-fdr</source>
98 <destination>$INSTALL_DIR/bin</destination>
99 </action>
100 <action type="move_file">
101 <source>rsem-generate-data-matrix</source>
102 <destination>$INSTALL_DIR/bin</destination>
103 </action>
104 <action type="move_file">
105 <source>rsem-generate-ngvector</source>
106 <destination>$INSTALL_DIR/bin</destination>
107 </action>
108 <action type="move_file">
109 <source>rsem-run-ebseq</source>
110 <destination>$INSTALL_DIR/bin</destination>
111 </action>
112 <action type="move_file">
113 <source>rsem-sam-validator</source>
114 <destination>$INSTALL_DIR/bin</destination>
115 </action>
116 <action type="move_file">
117 <source>rsem-scan-for-paired-end-reads</source>
118 <destination>$INSTALL_DIR/bin</destination>
119 </action>
120 <action type="move_file">
121 <source>rsem_perl_utils.pm</source>
122 <destination>$INSTALL_DIR/bin</destination>
123 </action>
124 <action type="set_environment_for_install">
125 <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
126 <package name="R_3_0_1" version="3.0.1" />
127 </repository>
128 </action>
129 <action type="shell_command">make ebseq</action>
130 <action type="make_directory">$INSTALL_DIR/bin/EBSeq</action>
131 <action type="move_directory_files">
132 <source_directory>EBSeq/EBSeq</source_directory>
133 <destination_directory>$INSTALL_DIR/bin/EBSeq</destination_directory>
134 </action>
135 <action type="move_directory_files">
136 <source_directory>EBSeq/blockmodeling</source_directory>
137 <destination_directory>$INSTALL_DIR/bin/EBSeq</destination_directory>
138 </action>
139 <action type="move_file">
140 <source>EBSeq/rsem-for-ebseq-find-DE</source>
141 <destination>$INSTALL_DIR/bin/EBSeq</destination>
142 </action>
143 <action type="move_file">
144 <source>EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info</source>
145 <destination>$INSTALL_DIR/bin/EBSeq</destination>
146 </action>
147 <action type="set_environment">
148 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
149 </action>
150 </actions>
151 </install>
152 <readme>
153 RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly
154 interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores,
155 variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95X credibility interval estimates for expression levels.
156 For visualization,It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files
157 can be visualized by both UCSC Genome browser and Broad InstituteXs Integrative Genomics Viewer (IGV).
158 Transcript-coordinate files can be visualized by IGV.
159
160 http://deweylab.biostat.wisc.edu/rsem/README.html
161 http://deweylab.biostat.wisc.edu/rsem/
162 </readme>
163 </package>
164 </tool_dependency>