From 0a43fb54fbdea0dd2220e3e60e4e3d299e296b22 Mon Sep 17 00:00:00 2001
From: Ke Hu <me@huke.info>
Date: Tue, 12 Apr 2016 10:51:15 -0400
Subject: [PATCH] update build and version infomation.

---
 .idea/modules/BSPAT_standAlone.iml      |  2 +-
 .idea/modules/BSPAT_standAlone_main.iml |  2 +-
 .idea/modules/BSPAT_standAlone_test.iml |  2 +-
 BSPAT_standAlone/README.md              |  1 +
 BSPAT_standAlone/build.gradle           | 17 ++++++++++-------
 BSPAT_standAlone/gradle.properties      |  4 ++++
 6 files changed, 18 insertions(+), 10 deletions(-)
 create mode 100644 BSPAT_standAlone/gradle.properties

diff --git a/.idea/modules/BSPAT_standAlone.iml b/.idea/modules/BSPAT_standAlone.iml
index 04d1b2b..1fc2369 100644
--- a/.idea/modules/BSPAT_standAlone.iml
+++ b/.idea/modules/BSPAT_standAlone.iml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<module external.linked.project.id="BSPAT_standAlone" external.linked.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.root.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.system.id="GRADLE" external.system.module.group="" external.system.module.version="0.1-beta" type="JAVA_MODULE" version="4">
+<module external.linked.project.id="BSPAT_standAlone" external.linked.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.root.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.system.id="GRADLE" external.system.module.group="" external.system.module.version="1.0.0-beta" type="JAVA_MODULE" version="4">
   <component name="NewModuleRootManager" inherit-compiler-output="true">
     <exclude-output />
     <content url="file://$MODULE_DIR$/../../BSPAT_standAlone">
diff --git a/.idea/modules/BSPAT_standAlone_main.iml b/.idea/modules/BSPAT_standAlone_main.iml
index 07cde32..146c31e 100644
--- a/.idea/modules/BSPAT_standAlone_main.iml
+++ b/.idea/modules/BSPAT_standAlone_main.iml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<module external.linked.project.id="BSPAT_standAlone:main" external.linked.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.root.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.system.id="GRADLE" external.system.module.group="" external.system.module.type="sourceSet" external.system.module.version="0.1-beta" type="JAVA_MODULE" version="4">
+<module external.linked.project.id="BSPAT_standAlone:main" external.linked.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.root.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.system.id="GRADLE" external.system.module.group="" external.system.module.type="sourceSet" external.system.module.version="1.0.0-beta" type="JAVA_MODULE" version="4">
   <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8" inherit-compiler-output="false">
     <output url="file://$MODULE_DIR$/../../BSPAT_standAlone/build/classes/main" />
     <exclude-output />
diff --git a/.idea/modules/BSPAT_standAlone_test.iml b/.idea/modules/BSPAT_standAlone_test.iml
index 144ee28..1394459 100644
--- a/.idea/modules/BSPAT_standAlone_test.iml
+++ b/.idea/modules/BSPAT_standAlone_test.iml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<module external.linked.project.id="BSPAT_standAlone:test" external.linked.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.root.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.system.id="GRADLE" external.system.module.group="" external.system.module.type="sourceSet" external.system.module.version="0.1-beta" type="JAVA_MODULE" version="4">
+<module external.linked.project.id="BSPAT_standAlone:test" external.linked.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.root.project.path="$MODULE_DIR$/../../BSPAT_standAlone" external.system.id="GRADLE" external.system.module.group="" external.system.module.type="sourceSet" external.system.module.version="1.0.0-beta" type="JAVA_MODULE" version="4">
   <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8" inherit-compiler-output="false">
     <output-test url="file://$MODULE_DIR$/../../BSPAT_standAlone/build/classes/test" />
     <exclude-output />
diff --git a/BSPAT_standAlone/README.md b/BSPAT_standAlone/README.md
index 01556f2..8c8023b 100644
--- a/BSPAT_standAlone/README.md
+++ b/BSPAT_standAlone/README.md
@@ -1,5 +1,6 @@
 BSPAT
 =====
+v1.0.0-beta
 
 # 1.Introduction
 BSPAT is a fast tool for analysing co-occurrence methylation patterns in bisulfite sequencing data.
diff --git a/BSPAT_standAlone/build.gradle b/BSPAT_standAlone/build.gradle
index a0fb1da..ba2f9a3 100644
--- a/BSPAT_standAlone/build.gradle
+++ b/BSPAT_standAlone/build.gradle
@@ -23,7 +23,7 @@ sourceSets {
     }
 }
 
-version '0.1-beta'
+version = theVersion
 
 repositories {
     jcenter()
@@ -62,16 +62,15 @@ CreateStartScripts buildStartScript(String appName, String mainClass, Iterable<S
 
 task addAllStartSctipts(dependsOn: jar) {
     group = "scripts"
-    buildStartScript('callBismark', 'edu.cwru.cbc.BSPAT.callBismark.CallBismark').execute()
-    buildStartScript('BSPAT', 'edu.cwru.cbc.BSPAT.CLI.BSPAT_pgm').execute()
-    buildStartScript('BSPAT_figure', 'edu.cwru.cbc.BSPAT.MethylFigure.MethylFigurePgm').execute()
+    buildStartScript(callBismark_appName, 'edu.cwru.cbc.BSPAT.callBismark.CallBismark').execute()
+    buildStartScript(BSPAT_appName, 'edu.cwru.cbc.BSPAT.CLI.BSPAT_pgm').execute()
+    buildStartScript(BSPAT_figure_appName, 'edu.cwru.cbc.BSPAT.MethylFigure.MethylFigurePgm').execute()
 }
 
 //noinspection GroovyAssignabilityCheck
 distributions {
     main {
         contents {
-            addAllStartSctipts
             into('bin') {
                 from 'build/scripts'
             }
@@ -81,17 +80,21 @@ distributions {
             }
             into('') {
                 from 'demo.zip'
+                from 'README.md'
+                from 'target_example.png'
             }
         }
     }
 }
 
-
 distZip.enabled = true
 distTar.enabled = false
 
+distZip.dependsOn addAllStartSctipts
+distZip.dependsOn test
+
 tasks.withType(Tar) {
     compression = Compression.GZIP
 }
 
-installDist.dependsOn build
\ No newline at end of file
+installDist.dependsOn distZip
\ No newline at end of file
diff --git a/BSPAT_standAlone/gradle.properties b/BSPAT_standAlone/gradle.properties
new file mode 100644
index 0000000..ba7b406
--- /dev/null
+++ b/BSPAT_standAlone/gradle.properties
@@ -0,0 +1,4 @@
+theVersion=1.0.0-beta
+BSPAT_appName=BSPAT
+callBismark_appName=callBismark
+BSPAT_figure_appName=BSPAT_figure
\ No newline at end of file