Skip to content

Commit

Permalink
first commit
Browse files Browse the repository at this point in the history
  • Loading branch information
@arnaudceol
arnaudceol committed Jun 10, 2015
1 parent d6654e9 commit de1c434
Show file tree
Hide file tree
Showing 172 changed files with 34,609 additions and 0 deletions.
3 changes: 3 additions & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
/target/
/.classpath
/.project
6 changes: 6 additions & 0 deletions mi-bundle/.gitignore
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
/.settings
/target
/.classpath
/.project
/nbactions.xml
/bin
18 changes: 18 additions & 0 deletions mi-bundle/nb-configuration.xml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
<?xml version="1.0" encoding="UTF-8"?>
<project-shared-configuration>
<!--
This file contains additional configuration written by modules in the NetBeans IDE.
The configuration is intended to be shared among all the users of project and
therefore it is assumed to be part of version control checkout.
Without this configuration present, some functionality in the IDE may be limited or fail altogether.
-->
<properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
<!--
Properties that influence various parts of the IDE, especially code formatting and the like.
You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
That way multiple projects can share the same settings (useful for formatting rules for example).
Any value defined here will override the pom.xml file value but is only applicable to the current project.
-->
<netbeans.hint.license>apache20</netbeans.hint.license>
</properties>
</project-shared-configuration>
294 changes: 294 additions & 0 deletions mi-bundle/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,294 @@
<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>it.iit.genomics.cru.mi</groupId>
<artifactId>igb-bundle</artifactId>
<packaging>bundle</packaging>
<version>2.8</version>

<!-- <parent>
<groupId>it.iit.genomics.cru.mi</groupId>
<artifactId>mi-master</artifactId>
<version>2.5-SNAPSHOT</version>
</parent>-->

<parent>
<groupId>it.iit.genomics.igb</groupId>
<artifactId>cru-igb-master</artifactId>
<version>8.3.1</version>
</parent>


<properties>
<bundle.symbolicName>it.iit.genomics.cru.mi.MIBundle</bundle.symbolicName>
<bundle.namespace>it.iit.genomics.cru.mi</bundle.namespace>
<genovizVersion>1.0.9</genovizVersion>
<jmol.version>14.2.2</jmol.version>
<bridges.version>2.2</bridges.version>
<cru.version>2.2-SNAPSHOT</cru.version>
<mi.version>2.7-SNAPSHOT</mi.version>
<netbeans.hint.license>apache20</netbeans.hint.license>
</properties>

<name>mi-bundle</name>

<build>
<finalName>MIBundle-igb${parent.version}-${version}</finalName>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.4.0</version>
<extensions>true</extensions>
<configuration>
<instructions>
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
<Bundle-Version>${version}</Bundle-Version>
<!-- <Bundle-Description>Map genomic regions to molecular interactions and structures. EPPIC version. For IGB v.${parent.version}</Bundle-Description>-->
<Bundle-Description>Map genomic regions to molecular interactions and structures. For IGB v.${parent.version}</Bundle-Description>
<Bundle-Author>Arnaud Ceol</Bundle-Author>
<!-- <Private-Package>it.iit.genomics.cru.*</Private-Package> -->
<Bundle-Activator>it.iit.genomics.cru.igb.bundles.mi.MIActivator</Bundle-Activator>
<Export-Package>org.apache.http.*</Export-Package>
<Import-Package>
*;resolution:=optional</Import-Package>
<Embed-Dependency>
uniprotkb, psimitab,
collections-generic,
commons-lang, biojava-core,commons-logging,
biojava-structure,biojava-alignment,
jmol,httpcore,httpclient,commons-httpclient,
interactome3d-bridge, cru-utils,
igb-commons,mi-structures, vecmath,
lucene-core,
lucene-analyzers-common,lucene-queries, lucene-queryparser,
JGoogleAnalyticsTracker,
dsysmap-bridge,
jung-graph-impl, jung-visualization,jung-api, jung-algorithms,
<!-- log4j-->
</Embed-Dependency>
<Embed-Transitive>true</Embed-Transitive>
<Export-Package/>
</instructions>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>org.apache.felix.dependencymanager.annotation</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<goals>
<goal>scan</goal>
</goals>
<configuration>
<log>info</log>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

<dependencies>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.1.1</version>
</dependency>
<!-- <dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>-->
<dependency>
<groupId>org.apache.felix</groupId>
<artifactId>org.apache.felix.http.bundle</artifactId>
<version>2.3.2</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.felix</groupId>
<artifactId>org.apache.felix.main</artifactId>
<version>4.2.2</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>genoviz</artifactId>
<version>${genovizVersion}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.lorainelab</groupId>
<artifactId>igb-genoviz-extensions-api</artifactId>
<version>${igb-version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>genometry</artifactId>
<version>${igb-version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>igb</artifactId>
<version>${igb-version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>igb-services-api</artifactId>
<version>${igb-version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>window-service</artifactId>
<version>${igb-version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>affymetrix-common</artifactId>
<version>${igb-version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.affymetrix</groupId>
<artifactId>igbSwingExt</artifactId>
<version>${igb-version}</version>
</dependency>


<dependency>
<groupId>psidev.psi.mi</groupId>
<artifactId>psimitab</artifactId>
<version>1.8.3</version>
<exclusions>
<exclusion>
<groupId>psidev.psi.mi</groupId>
<artifactId>psi25-xml</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.jmol</groupId>
<artifactId>jmol</artifactId>
<version>${jmol.version}</version>
</dependency>
<dependency>
<groupId>org.jmol</groupId>
<artifactId>jmol-lib</artifactId>
<version>${jmol.version}</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>org.utgenome.thirdparty</groupId>
<artifactId>picard</artifactId>
<version>1.86.0</version>
</dependency>
<dependency>
<groupId>commons-httpclient</groupId>
<artifactId>commons-httpclient</artifactId>
<version>3.1</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.1.3</version>
</dependency>
<dependency>
<groupId>it.iit.genomics.cru.bridges</groupId>
<artifactId>interactome3d-bridge</artifactId>
<version>${bridges.version}</version>
</dependency>
<dependency>
<groupId>it.iit.genomics.cru</groupId>
<artifactId>cru-utils</artifactId>
<version>${cru.version}</version>
</dependency>
<dependency>
<groupId>it.iit.genomics.cru.igb.bundles</groupId>
<artifactId>igb-commons</artifactId>
<version>${igb-version}</version>
</dependency>
<dependency>
<groupId>com.dmurph</groupId>
<artifactId>JGoogleAnalyticsTracker</artifactId>
<version>1.2.0</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>mi-structures</artifactId>
<version>${mi.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.7</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>it.iit.genomics.cru.bridges</groupId>
<artifactId>dsysmap-bridge</artifactId>
<version>${bridges.version}</version>
</dependency>
<dependency>
<groupId>net.sf.jung</groupId>
<artifactId>jung2</artifactId>
<version>2.0.1</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>net.sf.jung</groupId>
<artifactId>jung-graph-impl</artifactId>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>net.sf.jung</groupId>
<artifactId>jung-visualization</artifactId>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>net.sf.jung</groupId>
<artifactId>jung-api</artifactId>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>net.sf.jung</groupId>
<artifactId>jung-algorithms</artifactId>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>net.sourceforge.collections</groupId>
<artifactId>collections-generic</artifactId>
<version>4.01</version>
</dependency>
</dependencies>

<repositories>

<!-- EBI repositories - Where the IntAct artifacts are stored -->
<repository>
<id>ebi-repo</id>
<name>ebi-repo</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
</repository>

</repositories>
</project>
27 changes: 27 additions & 0 deletions mi-bundle/src/main/assembly/felix.xml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
<?xml version="1.0" encoding="UTF-8"?>
<assembly>
<id>all</id>
<formats>
<format>zip</format>
</formats>
<dependencySets>
<dependencySet>
<useProjectArtifact>false</useProjectArtifact>
<outputDirectory>modules</outputDirectory>
</dependencySet>
</dependencySets>
<files>
<file>
<source>${project.build.directory}/${project.build.finalName}.jar</source>
<outputDirectory>modules</outputDirectory>
</file>
<file>
<source>${project.build.directory}/felix.jar</source>
<outputDirectory>bin</outputDirectory>
</file>
<file>
<source>${project.build.directory}/config.properties</source>
<outputDirectory>conf</outputDirectory>
</file>
</files>
</assembly>
Loading

0 comments on commit de1c434

Please sign in to comment.