Merge pull request #40 from Integrative-Transcriptomics/dev

Dev

Author: Judith Neukamm

LICENSE

@@ -659,7 +659,7 @@ notice like this when it starts in an interactive mode:
 
 The hypothetical commands `show w' and `show c' should show the appropriate
 parts of the General Public License.  Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
+might be different; for a org.damageprofiler.GUI interface, you would use an "about box".
 
   You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.

README.md

@@ -85,6 +85,6 @@ Maximal value on y axis (Default: flexible, adapts to the calculated damage).
 
 
 
-Running the jar file without any parameter starts a GUI to configure the run.
+Running the jar file without any parameter starts a org.damageprofiler.GUI to configure the run.
 
 Stay tuned, a more detailed description, manual and tutorial of DamageProfiler is coming soon.

build.gradle

@@ -1,105 +1,104 @@
-group 'com.uni-tuebingen.de.it.eager.damageprofiler'
-version '0.4.9'
+ plugins {
+    id 'application'
+    id 'org.openjfx.javafxplugin' version '0.0.8'
+    id 'org.beryx.jlink' version '2.12.0'
+ }
 
-buildscript {
-    repositories {
-        jcenter()
-    }
-    dependencies {
-        classpath 'com.jfrog.bintray.gradle:gradle-bintray-plugin:1.8+'
-    }
-}
+version '0.5.0-java11'
 
 
-allprojects {
-    repositories {
-        jcenter()
-    }
-    apply plugin: 'maven'
-    apply plugin: 'maven-publish'
-    apply plugin: 'java'
-    apply plugin: 'idea'
-    apply plugin: 'com.jfrog.bintray'
-    apply plugin: 'jacoco'
+repositories {
+    mavenCentral()
+    jcenter()
 }
 
 
-sourceCompatibility = 1.8
-
-
-sourceSets {
-    main {
-        java {
-            srcDir 'src'
-        }
-    }
-}
-
+ javafx {
+     version = "14"
+     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.graphics', 'javafx.base', 'javafx.media', 'javafx.swing','javafx.web']
+ }
 
 dependencies {
+    compile group: 'log4j', name: 'log4j', version: '1.+'
     compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.+'
     compile group: 'commons-cli', name: 'commons-cli', version: '1.3.+'
     compile group: 'com.itextpdf', name: 'itextpdf', version: '5.5.+'
-    compile group: 'org.jfree', name: 'jcommon', version: '1.0.+'
-    compile group: 'jfree', name: 'jfreechart', version: '1.0.13'
     compile group: 'com.github.samtools', name: 'htsjdk', version: '2.+'
-    compile group: 'com.intellij', name: 'forms_rt', version: '6.0.+'
-    compile group: 'log4j', name: 'log4j', version: '1.+'
+    compile group: 'com.intellij', name: 'forms_rt', version: '5.+'
     compile group: 'com.github.broadinstitute', name: 'picard', version: '2.+'
+    compile group: 'org.jfree', name: 'jfreesvg', version: '2.0'
+    compile group: 'org.apache.commons', name: 'commons-text', version: '1.+'
+    compile 'org.jfree:jfreechart-fx:1.+'
 }
 
-
-
 jar {
     manifest {
-        attributes("Implementation-Title": "DamageProfiler",
-                "Implementation-Version": version, "main-Class": "RunDamageProfiler")
+        attributes 'Main-Class': 'RunDamageProfiler'
     }
-    doFirst {
-        from { configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) } }
+    from {
+        configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
     }
 }
 
 
-
-
-
-publishing {
-    publications {
-        MyPublication(MavenPublication) {
-            from components.java
-            groupId 'com.uni-tuebingen.de.it.eager'
-            artifactId 'DamageProfiler'
-        }
-    }
-}
-
-
-jacocoTestReport {
-    reports {
-        xml.enabled true
-    }
-}
-
-
-bintray {
-    user = System.getenv('BINTRAY_USER')
-	  key = System.getenv('BINTRAY_API_KEY')
-    publications = ['MyPublication']
-    publish = true
-    override = true
-    pkg {
-        repo = 'EAGER'
-        name = 'DamageProfiler'
-        licenses = ['GPL-3.0']
-        vcsUrl = "https://github.com/apeltzer/DamageProfiler"
-        version {
-            name = project.version
-            desc = 'Damage calculations for mapped reads.'
-            released  = new Date()
-            vcsTag = project.version
-            attributes = ['gradle-plugin': 'com.use.less:com.use.less.gradle:gradle-useless-plugin']
-        }
-
-    }
-}
+//// Uncomment when compiling with java8
+//version '0.5.0-java8'
+//buildscript {
+//    repositories {
+//        jcenter()
+//    }
+//    dependencies {
+//        classpath 'com.jfrog.bintray.gradle:gradle-bintray-plugin:1.8+'
+//    }
+//}
+//
+//allprojects {
+//    repositories {
+//        jcenter()
+//    }
+//    apply plugin: 'maven'
+//    apply plugin: 'maven-publish'
+//    apply plugin: 'java'
+//    apply plugin: 'idea'
+//    apply plugin: 'com.jfrog.bintray'
+//    apply plugin: 'jacoco'
+//}
+//
+//sourceCompatibility = 1.8
+//
+//sourceSets {
+//    main {
+//        java {
+//            srcDir 'src'
+//        }
+//
+//        resources {
+//            srcDirs "src/main/resources"
+//        }
+//    }
+//}
+//
+//
+//dependencies {
+//    compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.+'
+//    compile group: 'commons-cli', name: 'commons-cli', version: '1.3.+'
+//    compile group: 'com.itextpdf', name: 'itextpdf', version: '5.5.+'
+//    compile group: 'com.github.samtools', name: 'htsjdk', version: '2.+'
+//    compile group: 'com.intellij', name: 'forms_rt', version: '6.0.+'
+//    compile group: 'log4j', name: 'log4j', version: '1.+'
+//    compile group: 'com.github.broadinstitute', name: 'picard', version: '2.+'
+//    compile group: 'org.jfree', name: 'jfreesvg', version: '2.0'
+//    compile group: 'org.apache.commons', name: 'commons-text', version: '1.+'
+//    compile 'org.jfree:jfreechart-fx:1.+'
+//}
+//
+//
+//jar {
+//    manifest {
+//        attributes("Implementation-Title": "DamageProfiler",
+//                "Implementation-Version": version, "main-Class": "RunDamageProfiler")
+//    }
+//    doFirst {
+//        from { configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) } }
+//    }
+//}

docs/contents/generalUsage.rst

@@ -40,7 +40,7 @@ Options:
 
 
 DamageProfiler can be used in offline mode.
-Running the jar file without any parameter starts a GUI to configure the run.
+Running the jar file without any parameter starts a org.damageprofiler.GUI to configure the run.
 
 
 Log file