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author mytest
date Fri, 31 Jul 2015 03:25:28 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="trinityrnaseq" version="2013_08_14">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">http://tools.osdd.jnu.ac.in/ngsap/trinityrnaseq_r20140717.tar.gz</action>
7 <action type="shell_command">make</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 <action type="set_environment">
13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
14 </action>
15 <action type="set_environment">
16 <environment_variable name="TRINITY_HOME" action="set_to">$INSTALL_DIR</environment_variable>
17 </action>
18 </actions>
19 </install>
20 <readme>
21 </readme>
22 </package>
23 <package name="samtools" version="0.1.18">
24 <install version="1.0">
25 <actions_group>
26 <actions os="linux" architecture="i386">
27 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
28 <action type="move_directory_files">
29 <source_directory>.</source_directory>
30 <destination_directory>$INSTALL_DIR</destination_directory>
31 </action>
32 </actions>
33 <actions os="linux" architecture="x86_64">
34 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action>
35 <action type="move_directory_files">
36 <source_directory>.</source_directory>
37 <destination_directory>$INSTALL_DIR</destination_directory>
38 </action>
39 </actions>
40 <actions os="darwin" architecture="i386">
41 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
42 <action type="move_directory_files">
43 <source_directory>.</source_directory>
44 <destination_directory>$INSTALL_DIR</destination_directory>
45 </action>
46 </actions>
47 <actions os="darwin" architecture="x86_64">
48 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action>
49 <action type="move_directory_files">
50 <source_directory>.</source_directory>
51 <destination_directory>$INSTALL_DIR</destination_directory>
52 </action>
53 </actions>
54 <actions>
55 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2</action>
56 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
57 <action type="shell_command">make</action>
58 <action type="move_file">
59 <source>samtools</source>
60 <destination>$INSTALL_DIR/bin</destination>
61 </action>
62 <action type="move_file">
63 <source>libbam.a</source>
64 <destination>$INSTALL_DIR/lib</destination>
65 </action>
66 <action type="move_directory_files">
67 <source_directory>.</source_directory>
68 <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
69 </action>
70 </actions>
71 <action type="set_environment">
72 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
73 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
74 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
75 </action>
76 </actions_group>
77 </install>
78 <readme>
79 </readme>
80 </package>
81 <package name="rsem" version="1.1.17">
82 <install version="1.0">
83 <actions>
84 <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz</action>
85 <action type="shell_command">make</action>
86 <action type="make_directory">$INSTALL_DIR/bin/sam</action>
87 <action type="move_file">
88 <source>sam/samtools</source>
89 <destination>$INSTALL_DIR/bin/sam</destination>
90 </action>
91 <action type="move_file">
92 <source>convert-sam-for-rsem</source>
93 <destination>$INSTALL_DIR/bin</destination>
94 </action>
95 <action type="move_file">
96 <source>extract-transcript-to-gene-map-from-trinity</source>
97 <destination>$INSTALL_DIR/bin</destination>
98 </action>
99 <action type="move_file">
100 <source>rsem-bam2readdepth</source>
101 <destination>$INSTALL_DIR/bin</destination>
102 </action>
103 <action type="move_file">
104 <source>rsem-bam2wig</source>
105 <destination>$INSTALL_DIR/bin</destination>
106 </action>
107 <action type="move_file">
108 <source>rsem-build-read-index</source>
109 <destination>$INSTALL_DIR/bin</destination>
110 </action>
111 <action type="move_file">
112 <source>rsem-calculate-credibility-intervals</source>
113 <destination>$INSTALL_DIR/bin</destination>
114 </action>
115 <action type="move_file">
116 <source>rsem-calculate-expression</source>
117 <destination>$INSTALL_DIR/bin</destination>
118 </action>
119 <action type="move_file">
120 <source>rsem-extract-reference-transcripts</source>
121 <destination>$INSTALL_DIR/bin</destination>
122 </action>
123 <action type="move_file">
124 <source>rsem-gen-transcript-plots</source>
125 <destination>$INSTALL_DIR/bin</destination>
126 </action>
127 <action type="move_file">
128 <source>rsem-get-unique</source>
129 <destination>$INSTALL_DIR/bin</destination>
130 </action>
131 <action type="move_file">
132 <source>rsem-parse-alignments</source>
133 <destination>$INSTALL_DIR/bin</destination>
134 </action>
135 <action type="move_file">
136 <source>rsem-plot-model</source>
137 <destination>$INSTALL_DIR/bin</destination>
138 </action>
139 <action type="move_file">
140 <source>rsem-plot-transcript-wiggles</source>
141 <destination>$INSTALL_DIR/bin</destination>
142 </action>
143 <action type="move_file">
144 <source>rsem-prepare-reference</source>
145 <destination>$INSTALL_DIR/bin</destination>
146 </action>
147 <action type="move_file">
148 <source>rsem-preref</source>
149 <destination>$INSTALL_DIR/bin</destination>
150 </action>
151 <action type="move_file">
152 <source>rsem-run-em</source>
153 <destination>$INSTALL_DIR/bin</destination>
154 </action>
155 <action type="move_file">
156 <source>rsem-run-gibbs</source>
157 <destination>$INSTALL_DIR/bin</destination>
158 </action>
159 <action type="move_file">
160 <source>rsem-simulate-reads</source>
161 <destination>$INSTALL_DIR/bin</destination>
162 </action>
163 <action type="move_file">
164 <source>rsem-synthesis-reference-transcripts</source>
165 <destination>$INSTALL_DIR/bin</destination>
166 </action>
167 <action type="move_file">
168 <source>rsem-tbam2gbam</source>
169 <destination>$INSTALL_DIR/bin</destination>
170 </action>
171 <action type="set_environment">
172 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
173 </action>
174 </actions>
175 </install>
176 <readme>
177 </readme>
178 </package>
179 <package name="eXpress" version="1.5.1">
180 <install version="1.0">
181 <actions_group>
182 <actions os="linux" architecture="x86_64">
183 <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-linux_x86_64.tgz</action>
184 <action type="move_directory_files">
185 <source_directory>.</source_directory>
186 <destination_directory>$INSTALL_DIR/bin</destination_directory>
187 </action>
188 </actions>
189 <actions os="darwin" architecture="x86_64">
190 <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-macosx_x86_64.tgz</action>
191 <action type="move_directory_files">
192 <source_directory>.</source_directory>
193 <destination_directory>$INSTALL_DIR/bin</destination_directory>
194 </action>
195 </actions>
196 <actions>
197 <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz</action>
198 <action type="shell_command">cmake src -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL_DIR</action>
199 <action type="shell_command">make &amp;&amp; make install</action>
200 </actions>
201 <action type="set_environment">
202 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
203 </action>
204 </actions_group>
205 </install>
206 <readme></readme>
207 </package>
208 <package name="bowtie" version="0.12.7">
209 <install version="1.0">
210 <actions_group>
211 <actions os="linux" architecture="x86_64">
212 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz</action>
213 <action type="move_directory_files">
214 <source_directory>.</source_directory>
215 <destination_directory>$INSTALL_DIR</destination_directory>
216 </action>
217 </actions>
218 <actions os="darwin" architecture="x86_64">
219 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bowtie/bowtie-0.12.7-macos-10.5-x86_64.tgz</action>
220 <action type="move_directory_files">
221 <source_directory>.</source_directory>
222 <destination_directory>$INSTALL_DIR</destination_directory>
223 </action>
224 </actions>
225 <actions os="linux" architecture="i386">
226 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bowtie/bowtie-0.12.7-linux-i386.tgz</action>
227 <action type="move_directory_files">
228 <source_directory>.</source_directory>
229 <destination_directory>$INSTALL_DIR</destination_directory>
230 </action>
231 </actions>
232 <actions os="darwin" architecture="i386">
233 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/bowtie/bowtie-0.12.7-macos-10.5-i386.tgz</action>
234 <action type="move_directory_files">
235 <source_directory>.</source_directory>
236 <destination_directory>$INSTALL_DIR</destination_directory>
237 </action>
238 </actions>
239 <actions>
240 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
241 <action type="shell_command">make</action>
242 <action type="move_file">
243 <source>bowtie</source>
244 <destination>$INSTALL_DIR</destination>
245 </action>
246 <action type="move_file">
247 <source>bowtie-build</source>
248 <destination>$INSTALL_DIR</destination>
249 </action>
250 <action type="move_file">
251 <source>bowtie-inspect</source>
252 <destination>$INSTALL_DIR</destination>
253 </action>
254 </actions>
255 <action type="set_environment">
256 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
257 </action>
258 </actions_group>
259 </install>
260 <readme></readme>
261 </package>
262 <package name="bowtie2" version="2.1.0">
263 <install version="1.0">
264 <actions_group>
265 <actions os="linux" architecture="x86_64">
266 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz</action>
267 <action type="move_directory_files">
268 <source_directory>.</source_directory>
269 <destination_directory>$INSTALL_DIR</destination_directory>
270 </action>
271 </actions>
272 <actions os="darwin" architecture="x86_64">
273 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bowtie2/bowtie2-2.1.0-macos-x86_64.tgz</action>
274 <action type="move_directory_files">
275 <source_directory>.</source_directory>
276 <destination_directory>$INSTALL_DIR</destination_directory>
277 </action>
278 </actions>
279 <actions os="linux" architecture="i386">
280 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bowtie2/bowtie2-2.1.0-linux-i386.tgz</action>
281 <action type="move_directory_files">
282 <source_directory>.</source_directory>
283 <destination_directory>$INSTALL_DIR</destination_directory>
284 </action>
285 </actions>
286 <actions os="darwin" architecture="i386">
287 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/bowtie2/bowtie2-2.1.0-macos-i386.tgz</action>
288 <action type="move_directory_files">
289 <source_directory>.</source_directory>
290 <destination_directory>$INSTALL_DIR</destination_directory>
291 </action>
292 </actions>
293 <actions>
294 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
295 <action type="shell_command">make</action>
296 <action type="move_file">
297 <source>bowtie2</source>
298 <destination>$INSTALL_DIR</destination>
299 </action>
300 <action type="move_file">
301 <source>bowtie2-align</source>
302 <destination>$INSTALL_DIR</destination>
303 </action>
304 <action type="move_file">
305 <source>bowtie2-build</source>
306 <destination>$INSTALL_DIR</destination>
307 </action>
308 <action type="move_file">
309 <source>bowtie2-inspect</source>
310 <destination>$INSTALL_DIR</destination>
311 </action>
312 </actions>
313 <action type="set_environment">
314 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
315 </action>
316 </actions_group>
317 </install>
318 <readme></readme>
319 </package>
320 <package name="tophat2" version="2.0.9">
321 <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tophat2" owner="devteam" changeset_revision="ae06af1118dc" />
322 </package>
323 </tool_dependency>
324