Merge branch 'master' into dependabot/maven/junit-junit-4.13.1

.github/workflows/create-release.yml

@@ -0,0 +1,25 @@
+name: Create Release
+
+on: 
+  push:
+    tags:
+    - '*'
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK 11
+      uses: actions/setup-java@v2
+      with:
+        java-version: '11'
+        distribution: 'adopt'
+    - name: Build MIS
+      run: mvn install
+    - uses: ncipollo/release-action@v1
+      with:
+        allowUpdates: true
+        artifacts: "target/cloudgene-installer.sh"
+        token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/maven-test.yml

@@ -0,0 +1,23 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Maven Test
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK 11
+      uses: actions/setup-java@v2
+      with:
+        java-version: '11'
+        distribution: 'adopt'
+    - name: Run JUnit Tests
+      run: mvn install
+    - name: Upload coverage report to Codecov
+      uses: codecov/codecov-action@v2 

files/cloudgene

@@ -21,4 +21,4 @@ CLASS="cloudgene.mapred.CommandLineInterface"
 cd $FILE_PATH
 
 # execute cloudgene
-java -cp $CLASS_PATH $CLASS "$@"
+java -Dlog4j.configurationFile=config/log4j2.xml -cp $CLASS_PATH $CLASS "$@"