-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #1 from genepattern/develop
VisualizerLauncher_1.2.1
- Loading branch information
Showing
34 changed files
with
309 additions
and
4,688 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,7 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <classpath> | ||
| <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> | ||
| <classpathentry kind="src" path="src"/> | ||
| <classpathentry kind="src" path="lib"/> | ||
| <classpathentry kind="lib" path="lib/httpcore-4.4.4.jar"/> | ||
| <classpathentry kind="lib" path="lib/commons-codec-1.10.jar"/> | ||
| <classpathentry kind="lib" path="lib/httpclient-4.5.2.jar"/> | ||
| <classpathentry kind="lib" path="lib/commons-logging-1.2.jar"/> | ||
| <classpathentry kind="lib" path="lib/log4j-api-2.5.jar"/> | ||
| <classpathentry kind="lib" path="lib/log4j-core-2.5.jar"/> | ||
| <classpathentry kind="output" path="build/classes"/> | ||
| <classpathentry kind="src" output="target/classes" path="src/main/java"/> | ||
| <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/> | ||
| <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/> | ||
| <classpathentry kind="output" path="target/classes"/> | ||
| </classpath> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,3 +2,4 @@ | |
| *~ | ||
| /bin | ||
| /build | ||
| /target | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| Code signing is not integrated into the build script. At the Broad Institute we do something like ... | ||
|
|
||
| 1) create a zip file | ||
| cd target/VisualizerLauncher-1.2.1-SNAPSHOT-r2 | ||
| zip -r VisualizerLauncher.app.zip VisualizerLauncher.app | ||
|
|
||
| 2) copy it to remote server | ||
| scp VisualizerLauncher.app.zip <user>@<host>:~/visualizer-launcher | ||
|
|
||
| 3) sign the code | ||
| ssh <user>@<host> | ||
| cd ~/visualizer-launcher | ||
| mkdir dist | ||
| /sysman/scratch/teixeira/macsign/macsign.sh \ | ||
| -h xcode \ | ||
| -a `pwd`/VisualizerLauncher.app.zip \ | ||
| -d `pwd`/dist \ | ||
| -i /home/unix/genepatt/.ssh/id_rsa_genepatt \ | ||
| -u igvrole | ||
|
|
||
| 4) upload this to GitHub release |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| #maven.buildNumber.plugin properties file | ||
| buildNumber=1 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,254 @@ | ||
| <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/maven-v4_0_0.xsd" | ||
| > | ||
| <!-- | ||
| ================================================== | ||
| GenePattern Visualizer Launcher Maven Project | ||
| ================================================== | ||
| Usage: | ||
| # launch application (for debugging, testing) | ||
| mvn exec:exec | ||
| # package everything up for distribution | ||
| mvn package | ||
| --> | ||
|
|
||
| <modelVersion>4.0.0</modelVersion> | ||
| <groupId>genepattern.org</groupId> | ||
| <artifactId>VisualizerLauncher</artifactId> | ||
| <version>1.2.1</version> | ||
| <name>VisualizerLauncher</name> | ||
| <url>http://maven.apache.org</url> | ||
|
|
||
| <prerequisites> | ||
| <maven>3.0</maven> | ||
| </prerequisites> | ||
|
|
||
| <!-- dummy scm required for buildnumber-maven-plugin --> | ||
| <scm> | ||
| <connection>scm:svn:http://127.0.0.1/dummy</connection> | ||
| <developerConnection>scm:svn:https://127.0.0.1/dummy</developerConnection> | ||
| <tag>HEAD</tag> | ||
| <url>http://127.0.0.1/dummy</url> | ||
| </scm> | ||
|
|
||
| <build> | ||
| <!-- | ||
| <defaultGoal>clean package exec:exec</defaultGoal> | ||
| --> | ||
| <defaultGoal>package</defaultGoal> | ||
| <pluginManagement> | ||
| <plugins> | ||
| <plugin> | ||
| <groupId>org.codehaus.mojo</groupId> | ||
| <artifactId>buildnumber-maven-plugin</artifactId> | ||
| <version>1.4</version> | ||
| <executions> | ||
| <execution> | ||
| <id>buildnumber</id> | ||
| <phase>validate</phase> | ||
| <goals> | ||
| <goal>create</goal> | ||
| </goals> | ||
| </execution> | ||
| </executions> | ||
| <configuration> | ||
| <doCheck>false</doCheck> | ||
| <doUpdate>false</doUpdate> | ||
| <revisionOnScmFailure>unknownbuild</revisionOnScmFailure> | ||
| <format>{0,number}</format> | ||
| <items> | ||
| <item>buildNumber</item> | ||
| </items> | ||
| </configuration> | ||
| </plugin> | ||
| </plugins> | ||
| </pluginManagement> | ||
|
|
||
| <plugins> | ||
| <plugin> | ||
| <groupId>org.codehaus.mojo</groupId> | ||
| <artifactId>buildnumber-maven-plugin</artifactId> | ||
| </plugin> | ||
|
|
||
| <!-- Example: how to add an additional classpath element for junit tests --> | ||
| <!-- | ||
| <plugin> | ||
| <groupId>org.apache.maven.plugins</groupId> | ||
| <artifactId>maven-surefire-plugin</artifactId> | ||
| <version>2.12.4</version> | ||
| <configuration> | ||
| <additionalClasspathElements> | ||
| <additionalClasspathElement>${basedir}/src/test/lib/jdom.jar</additionalClasspathElement> | ||
| </additionalClasspathElements> | ||
| </configuration> | ||
| </plugin> | ||
| --> | ||
|
|
||
| <!-- | ||
| ================================================== | ||
| maven-assembly-plugin | ||
| ================================================== | ||
| Usage: | ||
| mvn clean compile assembly:single | ||
| To create an executable jar file which includes all library dependencies. | ||
| see: http://stackoverflow.com/questions/574594/how-can-i-create-an-executable-jar-with-dependencies-using-maven | ||
| --> | ||
| <plugin> | ||
| <artifactId>maven-assembly-plugin</artifactId> | ||
| <configuration> | ||
| <archive> | ||
| <manifest> | ||
| <mainClass>${mainClass}</mainClass> | ||
| </manifest> | ||
| </archive> | ||
| <descriptorRefs> | ||
| <descriptorRef>jar-with-dependencies</descriptorRef> | ||
| </descriptorRefs> | ||
| </configuration> | ||
| <executions> | ||
| <execution> | ||
| <id>make-assembly</id> <!-- this is used for inheritance merges --> | ||
| <phase>package</phase> <!-- bind to the packaging phase --> | ||
| <goals> | ||
| <goal>single</goal> | ||
| </goals> | ||
| </execution> | ||
| </executions> | ||
| </plugin> | ||
|
|
||
| <!-- | ||
| ================================================== | ||
| appbundle-maven-plugin (Mac OS X) | ||
| ================================================== | ||
| To package as a Mac OS X application bundle | ||
| see: https://github.com/federkasten/appbundle-maven-plugin | ||
| --> | ||
| <plugin> | ||
| <groupId>sh.tak.appbundler</groupId> | ||
| <artifactId>appbundle-maven-plugin</artifactId> | ||
| <version>1.2.0</version> | ||
| <configuration> | ||
| <mainClass>${mainClass}</mainClass> | ||
| </configuration> | ||
| <executions> | ||
| <execution> | ||
| <phase>package</phase> | ||
| <goals> | ||
| <goal>bundle</goal> | ||
| </goals> | ||
| </execution> | ||
| </executions> | ||
| </plugin> | ||
|
|
||
| <!-- | ||
| ================================================== | ||
| exec-maven-plugin | ||
| ================================================== | ||
| Run the VisualizerLauncher from the mvn command line. | ||
| Usage: | ||
| mvn -q clean package exec:exec | ||
| Note: '-q' means quiet, -X for debug output | ||
| --> | ||
| <plugin> | ||
| <groupId>org.codehaus.mojo</groupId> | ||
| <artifactId>exec-maven-plugin</artifactId> | ||
| <version>1.5.0</version> | ||
| <executions> | ||
| <execution> | ||
| <id>run-jar</id> | ||
| <phase>deploy</phase> | ||
| <goals> | ||
| <goal>exec</goal> | ||
| </goals> | ||
| </execution> | ||
| </executions> | ||
| <configuration> | ||
| <executable>java</executable> | ||
| <arguments> | ||
| <argument>-jar</argument> | ||
| <argument>${jarFile}</argument> | ||
| <!-- | ||
| <argument>-classpath</argument> | ||
| <classpath/> | ||
| <argument>${mainClass}</argument> | ||
| --> | ||
| </arguments> | ||
| </configuration> | ||
| </plugin> | ||
| </plugins> | ||
| <finalName>${project.artifactId}-${project.version}-SNAPSHOT-r${buildNumber}</finalName> | ||
| </build> | ||
|
|
||
| <properties> | ||
| <maven.compiler.source>1.7</maven.compiler.source> | ||
| <maven.compiler.target>1.7</maven.compiler.target> | ||
| <maven.build.timestamp.format>yyyy-MM-dd-HHmmss</maven.build.timestamp.format> | ||
|
|
||
| <mainClass>org.genepattern.desktop.VisualizerLauncher</mainClass> | ||
| <jarFile>target/${project.artifactId}-${project.version}-SNAPSHOT-r${buildNumber}-jar-with-dependencies.jar</jarFile> | ||
| </properties> | ||
|
|
||
| <dependencies> | ||
|
|
||
| <!-- https://mvnrepository.com/artifact/commons-codec/commons-codec --> | ||
| <dependency> | ||
| <groupId>commons-codec</groupId> | ||
| <artifactId>commons-codec</artifactId> | ||
| <version>1.10</version> | ||
| </dependency> | ||
|
|
||
| <!-- https://mvnrepository.com/artifact/commons-logging/commons-logging --> | ||
| <dependency> | ||
| <groupId>commons-logging</groupId> | ||
| <artifactId>commons-logging</artifactId> | ||
| <version>1.2</version> | ||
| </dependency> | ||
|
|
||
| <!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpclient --> | ||
| <dependency> | ||
| <groupId>org.apache.httpcomponents</groupId> | ||
| <artifactId>httpclient</artifactId> | ||
| <version>4.5.2</version> | ||
| </dependency> | ||
|
|
||
| <!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpcore --> | ||
| <dependency> | ||
| <groupId>org.apache.httpcomponents</groupId> | ||
| <artifactId>httpcore</artifactId> | ||
| <version>4.4.4</version> | ||
| </dependency> | ||
|
|
||
| <!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-api --> | ||
| <dependency> | ||
| <groupId>org.apache.logging.log4j</groupId> | ||
| <artifactId>log4j-api</artifactId> | ||
| <version>2.5</version> | ||
| </dependency> | ||
|
|
||
| <!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-core --> | ||
| <dependency> | ||
| <groupId>org.apache.logging.log4j</groupId> | ||
| <artifactId>log4j-core</artifactId> | ||
| <version>2.5</version> | ||
| </dependency> | ||
|
|
||
| <!-- https://mvnrepository.com/artifact/org.json/json --> | ||
| <dependency> | ||
| <groupId>org.json</groupId> | ||
| <artifactId>json</artifactId> | ||
| <version>20160810</version> | ||
| </dependency> | ||
|
|
||
| <!-- for testing --> | ||
| <dependency> | ||
| <groupId>junit</groupId> | ||
| <artifactId>junit</artifactId> | ||
| <version>4.12</version> | ||
| <scope>test</scope> | ||
| </dependency> | ||
|
|
||
| </dependencies> | ||
| </project> |
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
Oops, something went wrong.