diff --git a/BioArchLinux/beast2/PKGBUILD b/BioArchLinux/beast2/PKGBUILD
index a1c1ae6669..3b98a92842 100644
--- a/BioArchLinux/beast2/PKGBUILD
+++ b/BioArchLinux/beast2/PKGBUILD
@@ -1,5 +1,6 @@
 # Maintainer: Malacology <guoyizhang at malacology dot com>
 # Contributor: Malacology <guoyizhang at malacology dot com>
+# Contributor: sukanka <su975853527 at gmail dot com>
 
 pkgname=beast2
 pkgver=2.7.2
@@ -14,7 +15,7 @@ source=("${pkgname}-${pkgver}.tar.gz::https://github.com/CompEvol/beast2/archive
  "loganalyser.desktop" "${pkgname}-applauncher.desktop"
  # executable
  "${pkgname}-beauti" "${pkgname}-densitree" "${pkgname}-logcombiner" "${pkgname}-treeannotator" "${pkgname}-beast2"
- "${pkgname}-loganalyser" "${pkgname}-applauncher"
+ "${pkgname}-loganalyser" "${pkgname}-applauncher" "${pkgname}-packagemanager" "${pkgname}-environment"
 )
 sha256sums=('02f561f593adf54e512d34a9366dd9e4ed0b940cb4540d97a2b4e9b705f327a3'
             'SKIP'
@@ -25,19 +26,23 @@ sha256sums=('02f561f593adf54e512d34a9366dd9e4ed0b940cb4540d97a2b4e9b705f327a3'
             'df7bbf1363eec2af224251e77cd0a025003cd0ac751163a3e43cbe2bf52870d1'
             'e4b5398d4e5fe81b0e57b2e5d3a7b1d9621c97d1b8ce40a2d5b169bd94e89397'
             '8e999cabf53742fa818504a10f326e1275e23349f73267baba9058eda6add1ec'
-            'e8159c2a85ce43ea0d08ff4cf10525e5089db58a8c4f2bf9bfd0e368b4ecc099'
-            'f5cc878029b9d0469fa1db8a37a5f7e510871cc24ae6a24ecc011b5560f3bf9d'
-            '67785a6b1109f46203ff5f0169ed9d3f6118d72a3163e9141e10a24b1a10914f'
-            'aac5216b54d037f3cff3c76fa293c6afa08ed59e3e1865804f3af84569024e1e'
-            'ba9b05aac753a315c7ff373823cb752b535077209f4365a12a5e50d8742970f4'
-            '371a6a5b7ae241f77ef008984cf2b004d4d2aac373fe7dbe54ae9165c36f2c70'
-            '6efc50e2cf5e099f33634e702586e075fff4b34b9fc9f1a682b1c109e0343b85')
+            '6b935c9cd9eb7c901c2225083b92b410144eb67637443f54ba4bc99f1cd6bed1'
+            'ddcbeb065e1c9a1b0f745bb9df3dd2286bf5a3770f12b545962c5da33ccc3653'
+            'e9c61fd9798188e2153bfda533f7fbd4ae830cc6defe17847cbddf422873d054'
+            'e0b1931c484773b707b924b6014ee6e13b94abc47d37ccbf7b8d8af3befe4399'
+            'a6931ebff2b3f0cd8b8f99446ee0f93506cfe81fe8d254bd3f22a4e074a79588'
+            '34a6d929e0fc4d3e8d6bc68e6932a740c5193e37c321c231396168d7f4fc3a0e'
+            '3f2e227d433cdfdebe348eb3233b2b65497d8056a302fc95ecb1f2dbed7e1e77'
+            'a11c0a012cf96807a6d385e4503d480bca11855eecaab3f205c40e85efa721e7'
+            '0aef5826ec5523354216bdc9fe1342ee0dc39bf6d9e65e2ea8c9caad9fb5d843')
 depends=('java-runtime' 'java-openjfx')
 makedepends=('ant' 'git')
 optdepends=('beagle-lib')
 prepare(){
     cd ${srcdir}/${pkgname}-${pkgver}
     sed -i "s|2.7.1|2.7.2|" version.xml
+    cd lib
+    jar xvf beagle.jar
 }
 build(){
     cd "$srcdir/BeastFX"
@@ -47,7 +52,7 @@ build(){
         -Drelease_dir=release2 \
         -Dbeast2="../${pkgname}-${pkgver}" \
         -Dbeast2path="../${pkgname}-${pkgver}" \
-        -lib "/usr/lib/jvm/default-runtime/lib/" \
+        -lib "/usr/lib/jvm/default-runtime/lib" \
         -Dcommon_dir="../${pkgname}-${pkgver}/release/common/" \
         -DopenjreLnx="/usr/lib/jvm/default/"
 }
@@ -57,9 +62,18 @@ package() {
     cd "$srcdir/BeastFX/release2/Linux/"
     cp -rf beast/* "${pkgdir}/usr/share/${pkgname}"
 
+    # shipped modules
+    for module in {beastfx,beast,beagle}
+    do
+        install -d "${pkgdir}/usr/share/${pkgname}/lib/${module}"
+    done
+    cp -rf ${srcdir}/BeastFX/build/beastfx/* "${pkgdir}/usr/share/${pkgname}/lib/beastfx"
+    cp -rf ${srcdir}/${pkgname}-${pkgver}/build/beast/* "${pkgdir}/usr/share/${pkgname}/lib/beast"
+    cp -rf ${srcdir}/${pkgname}-${pkgver}/lib/beagle/*  "${pkgdir}/usr/share/${pkgname}/lib/beagle"
+
     # correct excutable
     rm -rf $pkgdir/usr/share/beast2/bin/*
-    for exe in {"beauti","densitree","logcombiner","treeannotator","beast2","loganalyser","applauncher"}
+    for exe in {"beauti","densitree","logcombiner","treeannotator","beast2","loganalyser","applauncher","packagemanager"}
     do
         install -Dm755 $srcdir/${pkgname}-${exe} -t $pkgdir/usr/share/beast2/bin/
     done
@@ -70,6 +84,8 @@ package() {
         ln -s /usr/share/beast2/bin/$bin ${pkgdir}/usr/bin/$bin
     done
     install -Dm 755 ${srcdir}/*.desktop -t ${pkgdir}/usr/share/applications
+    # Do NOT put link this file to /usr/bin
+    install -Dm755 $srcdir/${pkgname}-environment -t $pkgdir/usr/share/beast2/bin/
 
     # clear files
     rm -rf $pkgdir/usr/share/beast2/jre
diff --git a/BioArchLinux/beast2/beast2-applauncher b/BioArchLinux/beast2/beast2-applauncher
index 1b7a24288c..e2807c046c 100755
--- a/BioArchLinux/beast2/beast2-applauncher
+++ b/BioArchLinux/beast2/beast2-applauncher
@@ -1,18 +1,18 @@
 #!/bin/sh
-export JAVA_HOME=/usr/lib/jvm/default
-export BEAST=/usr/share/beast2
-
-BEAST_LIB="$BEAST/lib"
-
-JAVA="$JAVA_HOME"/bin/java
-
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
+self_path=$(realpath $0)
+environment_file=$(dirname $self_path)/beast2-environment
+source $environment_file
 
 # use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
 # this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
-  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
+  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    beast.pkgmgmt.launcher.AppLauncherLauncher $*
 else
-  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
+  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml,javafx.web,javafx.media \
+    beast.pkgmgmt.launcher.AppLauncherLauncher $*
 fi
diff --git a/BioArchLinux/beast2/beast2-beast2 b/BioArchLinux/beast2/beast2-beast2
index 543775a333..3ef34e4b6f 100755
--- a/BioArchLinux/beast2/beast2-beast2
+++ b/BioArchLinux/beast2/beast2-beast2
@@ -1,12 +1,9 @@
 #!/bin/sh
-export JAVA_HOME=/usr/lib/jvm/default
-export BEAST=/usr/share/beast2
+self_path=$(realpath $0)
+environment_file=$(dirname $self_path)/beast2-environment
+source $environment_file
 
-BEAST_LIB="$BEAST/lib"
-
-JAVA="$JAVA_HOME"/bin/java
-
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
-
-"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$LD_LIBRARY_PATH" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.BeastLauncher $*
+"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    beast.pkgmgmt.launcher.BeastLauncher $*
diff --git a/BioArchLinux/beast2/beast2-beauti b/BioArchLinux/beast2/beast2-beauti
index 6d24621260..151d4c9407 100755
--- a/BioArchLinux/beast2/beast2-beauti
+++ b/BioArchLinux/beast2/beast2-beauti
@@ -1,12 +1,9 @@
 #!/bin/sh
-export JAVA_HOME=/usr/lib/jvm/default
-export BEAST=/usr/share/beast2
+self_path=$(realpath $0)
+environment_file=$(dirname $self_path)/beast2-environment
+source $environment_file
 
-BEAST_LIB="$BEAST/lib"
-
-JAVA="$JAVA_HOME"/bin/java
-
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
-
-"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.BeautiLauncher -capture $*
+"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml,javafx.web,javafx.media \
+    beast.pkgmgmt.launcher.BeautiLauncher -capture $*
diff --git a/BioArchLinux/beast2/beast2-densitree b/BioArchLinux/beast2/beast2-densitree
index 2bdf76f791..c4e4c81a51 100755
--- a/BioArchLinux/beast2/beast2-densitree
+++ b/BioArchLinux/beast2/beast2-densitree
@@ -1,12 +1,9 @@
 #!/bin/sh
-export JAVA_HOME=/usr/lib/jvm/default
-export BEAST=/usr/share/beast2
+self_path=$(realpath $0)
+environment_file=$(dirname $self_path)/beast2-environment
+source $environment_file
 
-BEAST_LIB="$BEAST/lib"
-
-JAVA="$JAVA_HOME"/bin/java
-
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
-
-"$JAVA" -Xms256m -Xmx8g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/DensiTree.jar:$BEAST/DensiTree.app/Contents/Resources/Java/DensiTree.jar" viz.DensiTree $*
+"$JAVA" -Xms256m -Xmx8g -Djava.library.path="$BEAST_LIB" \
+    -cp "$BEAST_LIB/DensiTree.jar:$BEAST/DensiTree.app/Contents/Resources/Java/DensiTree.jar" \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    viz.DensiTree $*
diff --git a/BioArchLinux/beast2/beast2-environment b/BioArchLinux/beast2/beast2-environment
new file mode 100644
index 0000000000..e2996d2773
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-environment
@@ -0,0 +1,15 @@
+#!/bin/sh
+
+# General environment for beast2
+
+export JAVA_HOME=${JAVA_HOME:-/usr/lib/jvm/default}
+export BEAST=/usr/share/beast2
+JFX="$JAVA_HOME/lib"
+export JFX_LIBS="$JFX/javafx.controls.jar:$JFX/javafx.fxml.jar:$JFX/javafx.graphics.jar:$JFX/javafx.base.jar:$JFX/javafx.web.jar:$JFX/javafx.media.jar"
+export BEAST_LIB="$BEAST/lib"
+export DEFAULT_CP="/usr/share/beast2/lib"
+
+export JAVA="$JAVA_HOME"/bin/java
+
+# use BEAGLE_LIB if the BEAGLE library is not in a standard location
+export BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
diff --git a/BioArchLinux/beast2/beast2-loganalyser b/BioArchLinux/beast2/beast2-loganalyser
index 21cc2c9dfa..a3e788e99e 100755
--- a/BioArchLinux/beast2/beast2-loganalyser
+++ b/BioArchLinux/beast2/beast2-loganalyser
@@ -1,16 +1,18 @@
 #!/bin/sh
-export JAVA_HOME=/usr/lib/jvm/default
-export BEAST=/usr/share/beast2
-
-BEAST_LIB="$BEAST/lib"
-JAVA="$JAVA_HOME"/bin/java
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
+self_path=$(realpath $0)
+environment_file=$(dirname $self_path)/beast2-environment
+source $environment_file
 
 # use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
 # this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
-  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
+  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
 else
-  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
+  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
 fi
diff --git a/BioArchLinux/beast2/beast2-logcombiner b/BioArchLinux/beast2/beast2-logcombiner
index 543302c2c0..524a21da15 100755
--- a/BioArchLinux/beast2/beast2-logcombiner
+++ b/BioArchLinux/beast2/beast2-logcombiner
@@ -1,12 +1,9 @@
 #!/bin/sh
-export JAVA_HOME=/usr/lib/jvm/default
-export BEAST=/usr/share/beast2
+self_path=$(realpath $0)
+environment_file=$(dirname $self_path)/beast2-environment
+source $environment_file
 
-BEAST_LIB="$BEAST/lib"
-
-JAVA="$JAVA_HOME"/bin/java
-
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
-
-"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.LogCombinerLauncher $*
+"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    beast.pkgmgmt.launcher.LogCombinerLauncher $*
diff --git a/BioArchLinux/beast2/beast2-packagemanager b/BioArchLinux/beast2/beast2-packagemanager
index 0c9113e2e2..863e0b455e 100755
--- a/BioArchLinux/beast2/beast2-packagemanager
+++ b/BioArchLinux/beast2/beast2-packagemanager
@@ -1,11 +1,9 @@
 #!/bin/sh
-export JAVA_HOME=/usr/lib/jvm/default
-export BEAST=/usr/share/beast2
+self_path=$(realpath $0)
+environment_file=$(dirname $self_path)/beast2-environment
+source $environment_file
 
-BEAST_LIB="$BEAST/lib"
-
-JAVA="$JAVA_HOME"/bin/java
-
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
-"$JAVA" -Xms256m -Xmx8g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.PackageManager $*
+"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    beast.pkgmgmt.PackageManager $*
diff --git a/BioArchLinux/beast2/beast2-treeannotator b/BioArchLinux/beast2/beast2-treeannotator
index dd2d6f638c..0af2fa22a5 100755
--- a/BioArchLinux/beast2/beast2-treeannotator
+++ b/BioArchLinux/beast2/beast2-treeannotator
@@ -1,11 +1,9 @@
 #!/bin/sh
-export JAVA_HOME=/usr/lib/jvm/default
-export BEAST=/usr/share/beast2
+self_path=$(realpath $0)
+environment_file=$(dirname $self_path)/beast2-environment
+source $environment_file
 
-BEAST_LIB="$BEAST/lib"
-
-JAVA="$JAVA_HOME"/bin/java
-
-# use BEAGLE_LIB if the BEAGLE library is not in a standard location
-BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
-"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.TreeAnnotatorLauncher $*
+"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
+    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
+    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    beast.pkgmgmt.launcher.TreeAnnotatorLauncher $*