-
Notifications
You must be signed in to change notification settings - Fork 1
/
pom.xml
418 lines (409 loc) · 13.3 KB
/
pom.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
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>es.cnio.bioinfo</groupId>
<artifactId>bicycle</artifactId>
<version>1.8.2</version>
<description>bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis. More info at the [bicycle](http://sing.ei.uvigo.es/bicycle) project page.</description>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.target>1.8</maven.compiler.target>
<maven.compiler.source>1.8</maven.compiler.source>
<apache.math.version>3.6</apache.math.version>
<sing.math.version>0.1-SNAPSHOT</sing.math.version>
<junit.version>4.12</junit.version>
<easymock.version>3.4</easymock.version>
<maven-assembly-plugin.version>2.2</maven-assembly-plugin.version>
<dist.directory>${project.build.directory}/dist</dist.directory>
</properties>
<developers>
<developer>
<name>Daniel Glez-Peña (SING Research Group. Informatics Department. University of Vigo)</name>
</developer>
<developer>
<name>Osvaldo Graña (Bioinformatics Unit. CNIO: Spanish National Cancer Research Centre)</name>
</developer>
<developer>
<name>Hugo López-Fernández (SING Research Group. Informatics Department. University of Vigo)</name>
</developer>
</developers>
<licenses>
<license>
<name>GNU Lesser General Public License v3.0</name>
</license>
</licenses>
<repositories>
<repository>
<id>sing-repository</id>
<name>SING repository</name>
<url>http://sing.ei.uvigo.es/maven2</url>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>sing-repository</id>
<name>SING repository</name>
<url>http://sing.ei.uvigo.es/maven2</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>true</enabled>
</releases>
</pluginRepository>
<pluginRepository>
<id>sonatype-public-repository</id>
<url>https://oss.sonatype.org/content/groups/public</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>true</enabled>
</releases>
</pluginRepository>
</pluginRepositories>
<dependencies>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>${apache.math.version}</version>
</dependency>
<dependency>
<groupId>es.uvigo.ei.sing.thirdparty</groupId>
<artifactId>picard</artifactId>
<version>1.55.985</version>
</dependency>
<dependency>
<groupId>es.uvigo.ei.sing.thirdparty</groupId>
<artifactId>gatk-legacy-singpatched-nojavassist</artifactId>
<version>1.3.1</version>
</dependency>
<dependency>
<groupId>es.uvigo.ei.sing</groupId>
<artifactId>pileline-tools</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>es.uvigo.ei.sing</groupId>
<artifactId>pileline-tools-tests</artifactId>
<version>1.0.5</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.20.0-GA</version>
</dependency>
<dependency>
<groupId>es.uvigo.ei.sing</groupId>
<artifactId>math</artifactId>
<version>${sing.math.version}</version>
</dependency>
<dependency>
<groupId>org.easymock</groupId>
<artifactId>easymock</artifactId>
<version>${easymock.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.txt</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<excludes>
<exclude>**/*.txt</exclude>
</excludes>
</resource>
<resource>
<directory>src/main/resources/assembly</directory>
<filtering>true</filtering>
<includes>
<include>README.txt</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.7</version>
<executions>
<execution>
<id>copy-resources</id>
<!-- here the phase you need -->
<phase>validate</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${dist.directory}/cmd</outputDirectory>
<resources>
<resource>
<directory>${project.build.resources[0].directory}/cmd</directory>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
<execution>
<id>copy-resources-2</id>
<!-- here the phase you need -->
<phase>validate</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${dist.directory}</outputDirectory>
<resources>
<resource>
<directory>${project.build.resources[0].directory}/assembly</directory>
<includes>
<include>README.txt</include>
</includes>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
<executions>
<execution>
<id>copy-dependencies</id>
<!-- here the phase you need -->
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${dist.directory}/lib</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.5</version>
<configuration>
<systemPropertyVariables>
<java.io.tmpdir>${project.build.directory}</java.io.tmpdir>
<bowtie.path>${bowtie.path}</bowtie.path>
<bowtie2.path>${bowtie2.path}</bowtie2.path>
<samtools.path>${samtools.path}</samtools.path>
</systemPropertyVariables>
<useSystemClassLoader>false</useSystemClassLoader>
<excludes>
<exclude>**/testsimulated/*Test.java</exclude>
</excludes>
</configuration>
<executions>
<execution>
<id>simulation-test</id>
<phase>test</phase>
<goals>
<goal>test</goal>
</goals>
<configuration>
<skip>${skipSimulatedTests}</skip>
<excludes>
<exclude>**/test/*Test.java</exclude>
</excludes>
<includes>
<include>**/testsimulated/*Test.java</include>
</includes>
</configuration>
</execution>
</executions>
</plugin>
<!--<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.5</version>
<configuration>
<systemPropertyVariables>
<java.io.tmpdir>${project.build.directory}</java.io.tmpdir>
<bowtie.path>${bowtie.path}</bowtie.path>
<samtools.path>${samtools.path}</samtools.path>
</systemPropertyVariables>
<useSystemClassLoader>false</useSystemClassLoader>
<excludes>
<exclude>**/testsimulated/*Test.java</exclude>
</excludes>
</configuration>
</plugin>-->
<!--<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.1</version>
<configuration>
<outputDirectory>${dist.directory}</outputDirectory>
</configuration>
</plugin>-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.1</version>
<configuration>
<outputDirectory>${dist.directory}</outputDirectory>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>es.cnio.bioinfo.bicycle.cli.Main</mainClass>
<useUniqueVersions>false</useUniqueVersions>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.6</version>
<executions>
<execution>
<id>set-execution-permissions-bicycle</id>
<phase>package</phase>
<configuration>
<target>
<chmod file="${dist.directory}/cmd/bicycle" perm="755" />
</target>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.googlecode.maven-download-plugin</groupId>
<artifactId>download-maven-plugin</artifactId>
<version>1.2.1</version>
<executions>
<execution>
<id>download-simulated-test-dataset</id>
<phase>process-test-resources</phase>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<skip>${skipSimulatedTests}</skip>
<url>http://sing.ei.uvigo.es/bicycle/downloads/sample-test-data-1.6.zip</url>
<unpack>true</unpack>
<outputDirectory>${project.build.directory}/test-classes</outputDirectory>
<md5>7094bbab8a42a2b98ece343872a8c2be</md5>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>${maven-assembly-plugin.version}</version>
<configuration>
<finalName>${project.name}-${project.version}</finalName>
<appendAssemblyId>true</appendAssemblyId>
<outputDirectory>${project.builds.directory}</outputDirectory>
<descriptors>
<descriptor>src/main/resources/assembly/linux.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>distribution</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.mule.tools</groupId>
<artifactId>github-readme-maven-plugin</artifactId>
<version>1.0-SNAPSHOT</version>
<executions>
<execution>
<phase>install</phase>
<goals>
<goal>generate</goal>
</goals>
<configuration>
<sections>
<section><![CDATA[
## How it works?
**bicycle** (_**bi**sulfite-based methyl**cy**tosine **c**al**le**r_) is a next-generation sequencing bioinformatic pipeline aimed to analyze whole genome bisulfite sequencing data. It can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols, and from single-end and paired-end sequencing, and performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH).
**bicycle** uses as input the bisulfite sequencing files from the different samples (FASTQ format) and a reference genome (FASTA format). It then performs: **generation and indexing of Watson and Crick bisulfited versions of the reference genome**, **in-silico bisulfitation of sequenced reads**, **read alignment**, **error estimation in bisulfite conversion**, **identification of clonal and ambiguous reads**, **cytosine methylation detection in CG and non-CG contexts, with non-CG to CG context correction when appropriated**, **calculates methylation ratios, beta scores and weighted mean of cytosine methylation status**, and performs **genomic annotation of methylated regions**, and **differential methylation for cytosines (DMC) and genomic regions (DMR)**.
]]></section>
<section><![CDATA[
## Requirements
Bicycle requirements:
- Operating System: Linux/OSX
- Java 1.8+
- Bowtie1 aligner 0.12.7+ or Bowtie2 aligner 2.3.2+
- samtools 0.1.8+
]]></section>
<section><. Informatics Department. University of Vigo)
- David Pisano ([Bioinformatics Unit](http://www.cnio.es/es/grupos/plantillas/presentacion.asp?grupo=50004300). CNIO: Spanish National Cancer Research Centre)
]]></section>
</sections>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<!--This plugin's configuration is used to store Eclipse m2e settings
only. It has no influence on the Maven build itself. -->
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>
com.googlecode.maven-download-plugin
</groupId>
<artifactId>
download-maven-plugin
</artifactId>
<versionRange>
[1.2.1,)
</versionRange>
<goals>
<goal>wget</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore></ignore>
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>