forked from bg7/BG7
-
Notifications
You must be signed in to change notification settings - Fork 0
/
build.xml
314 lines (301 loc) · 15.1 KB
/
build.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
<?xml version="1.0" encoding="UTF-8"?>
<!-- You may freely edit this file. See commented blocks below for -->
<!-- some examples of how to customize the build. -->
<!-- (If you delete it and reopen the project it will be recreated.) -->
<!-- By default, only the Clean and Build commands use this build script. -->
<!-- Commands such as Run, Debug, and Test only use this build script if -->
<!-- the Compile on Save feature is turned off for the project. -->
<!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
<!-- in the project's Project Properties dialog box.-->
<project name="BG7" default="default" basedir=".">
<description>Builds, tests, and runs the project BG7.</description>
<import file="nbproject/build-impl.xml"/>
<!--
There exist several targets which are by default empty and which can be
used for execution of your tasks. These targets are usually executed
before and after some main targets. They are:
-pre-init: called before initialization of project properties
-post-init: called after initialization of project properties
-pre-compile: called before javac compilation
-post-compile: called after javac compilation
-pre-compile-single: called before javac compilation of single file
-post-compile-single: called after javac compilation of single file
-pre-compile-test: called before javac compilation of JUnit tests
-post-compile-test: called after javac compilation of JUnit tests
-pre-compile-test-single: called before javac compilation of single JUnit test
-post-compile-test-single: called after javac compilation of single JUunit test
-pre-jar: called before JAR building
-post-jar: called after JAR building
-post-clean: called after cleaning build products
(Targets beginning with '-' are not intended to be called on their own.)
Example of inserting an obfuscator after compilation could look like this:
<target name="-post-compile">
<obfuscate>
<fileset dir="${build.classes.dir}"/>
</obfuscate>
</target>
For list of available properties check the imported
nbproject/build-impl.xml file.
Another way to customize the build is by overriding existing main targets.
The targets of interest are:
-init-macrodef-javac: defines macro for javac compilation
-init-macrodef-junit: defines macro for junit execution
-init-macrodef-debug: defines macro for class debugging
-init-macrodef-java: defines macro for class execution
-do-jar-with-manifest: JAR building (if you are using a manifest)
-do-jar-without-manifest: JAR building (if you are not using a manifest)
run: execution of project
-javadoc-build: Javadoc generation
test-report: JUnit report generation
An example of overriding the target for project execution could look like this:
<target name="run" depends="PrediccionGenes-impl.jar">
<exec dir="bin" executable="launcher.exe">
<arg file="${dist.jar}"/>
</exec>
</target>
Notice that the overridden target depends on the jar target and not only on
the compile target as the regular run target does. Again, for a list of available
properties which you can use, check the target you are overriding in the
nbproject/build-impl.xml file.
-->
<!-- <target name="-post-jar">
<jar jarfile="jars/RemoveDismissedGenes.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.RemoveDismissedGenes"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/ExportGenBankFiles.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.gb.ExportGenBankFiles"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/Export5ColumnsGenBankFiles.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.gb.Export5ColumnsGenBankFiles"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/Control5ColumnsGenBankFilesQuality.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.gb.Control5ColumnsGenBankFilesQuality"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/ImportGeneBankFiles.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.gb.ImportGeneBankFiles"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/ControlGenBankFilesQuality.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.gb.ControlGenBankFilesQuality"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/PredictGenes.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.PredictGenes"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/RemoveDuplicatedGenes.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.RemoveDuplicatedGenes"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/SolveOverlappings.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.SolveOverlappings"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/ExportEmblFiles.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.embl.ExportEmblFiles"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/FillDataFromUniprot.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/commons-httpclient-3.1.jar" excludes="META-INF/*" />
<zipfileset src="lib/commons-logging-1.1.1.jar" excludes="META-INF/*" />
<zipfileset src="lib/commons-codec-1.4.jar" excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.FillDataFromUniprot"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/GenerateFastaFiles.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.GenerateFastaFiles"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/GenerateCSVFile.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.GenerateCSVFile"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/GenerateGffFile.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.GenerateGffFile"/>
</manifest>
</jar>
</target>-->
<target name="-post-jar">
<jar jarfile="jars/BG7.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/commons-httpclient-3.1.jar" excludes="META-INF/*" />
<zipfileset src="lib/commons-logging-1.1.1.jar" excludes="META-INF/*" />
<zipfileset src="lib/commons-codec-1.4.jar" excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.BG7"/>
</manifest>
</jar>
</target>
<!-- <target name="-post-jar">
<jar jarfile="jars/AutomaticQualityControl.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.AutomaticQualityControl"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/BasicQualityControl.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.BasicQualityControl"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/GetIntergenicSequences.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/Era7BioinfoXML-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.GetIntergenicSequences"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/FixFastaHeaders.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.FixFastaHeaders"/>
</manifest>
</jar>
</target>-->
<!-- <target name="-post-jar">
<jar jarfile="jars/FixFastaHeadersQC.jar">
<zipfileset src="${dist.jar}" excludes="META-INF/*" />
<zipfileset src="lib/BioinfoUtil-1.0-jar-with-dependencies.jar"
excludes="META-INF/*" />
<manifest>
<attribute name="Main-Class" value="com.era7.bioinfo.annotation.FixFastaHeadersQC"/>
</manifest>
</jar>
</target>-->
</project>