From 513c1fdc0ef83cd3e0da7f2bbf09254f512f173d Mon Sep 17 00:00:00 2001
From: sukanka <su975853527@gmail.com>
Date: Tue, 1 Nov 2022 22:06:42 +0800
Subject: [PATCH] beast2: fix some issues

---
 BioArchLinux/beast2/PKGBUILD                  | 53 ++++++++++++++-----
 BioArchLinux/beast2/beast2-applauncher        | 18 +++++++
 ...her.desktop => beast2-applauncher.desktop} |  2 +-
 BioArchLinux/beast2/beast2-beast2             | 12 +++++
 BioArchLinux/beast2/beast2-beauti             | 12 +++++
 BioArchLinux/beast2/beast2-densitree          | 12 +++++
 BioArchLinux/beast2/beast2-loganalyser        | 16 ++++++
 BioArchLinux/beast2/beast2-logcombiner        | 12 +++++
 BioArchLinux/beast2/beast2-packagemanager     | 11 ++++
 BioArchLinux/beast2/beast2-treeannotator      | 11 ++++
 BioArchLinux/beast2/beast2.desktop            |  2 +-
 BioArchLinux/beast2/beauti.desktop            |  2 +-
 BioArchLinux/beast2/densitree.desktop         |  2 +-
 BioArchLinux/beast2/loganalyser.desktop       |  2 +-
 BioArchLinux/beast2/logcombiner.desktop       |  2 +-
 BioArchLinux/beast2/treeannotator.desktop     |  2 +-
 16 files changed, 150 insertions(+), 21 deletions(-)
 create mode 100755 BioArchLinux/beast2/beast2-applauncher
 rename BioArchLinux/beast2/{applauncher.desktop => beast2-applauncher.desktop} (87%)
 create mode 100755 BioArchLinux/beast2/beast2-beast2
 create mode 100755 BioArchLinux/beast2/beast2-beauti
 create mode 100755 BioArchLinux/beast2/beast2-densitree
 create mode 100755 BioArchLinux/beast2/beast2-loganalyser
 create mode 100755 BioArchLinux/beast2/beast2-logcombiner
 create mode 100755 BioArchLinux/beast2/beast2-packagemanager
 create mode 100755 BioArchLinux/beast2/beast2-treeannotator

diff --git a/BioArchLinux/beast2/PKGBUILD b/BioArchLinux/beast2/PKGBUILD
index be683c7cbd..a1c1ae6669 100644
--- a/BioArchLinux/beast2/PKGBUILD
+++ b/BioArchLinux/beast2/PKGBUILD
@@ -11,23 +11,38 @@ license=('LGPL')
 source=("${pkgname}-${pkgver}.tar.gz::https://github.com/CompEvol/beast2/archive/refs/tags/${pkgver}.tar.gz"
 "git+https://github.com/CompEvol/BeastFX.git#commit=e6c9fdb2"
  "beauti.desktop" "densitree.desktop" "logcombiner.desktop" "treeannotator.desktop" "beast2.desktop"
- "loganalyser.desktop" "applauncher.desktop"
+ "loganalyser.desktop" "${pkgname}-applauncher.desktop"
+ # executable
+ "${pkgname}-beauti" "${pkgname}-densitree" "${pkgname}-logcombiner" "${pkgname}-treeannotator" "${pkgname}-beast2"
+ "${pkgname}-loganalyser" "${pkgname}-applauncher"
 )
 sha256sums=('02f561f593adf54e512d34a9366dd9e4ed0b940cb4540d97a2b4e9b705f327a3'
             'SKIP'
-            '83fba4c776fd29d6852c9c412c31d98bff657e2d2d2763dfe46d4c6174a9495f'
-            '40d86086691b6cb91d0af54e5dc53d6693e084242ff3cc77862650ca78667c3d'
-            'c2057c6ac656e13dcfbdf580a696bc79cb22c3d5270d546eac3e2fb42d620f20'
-            '960a2d9030105156e178fe8fd5a8329cf10af1e16141623da47f649f059906b0'
-            'cf09789425aec65601f8dc585a9e5afd0f43af713ce67d8009b18efef5b6edd3'
-            'b10a94df8d6c44b270cd8ea6f9af08ac803ff0a210aae602b80bbb99050f5b46'
-            '78671538afa07e8efac47eadc845c1616d553e095bf749c0215fdba8af2a2c1b')
+            'f35255c946a105a60e81fcf44ed3f5c28e6903f0e9cedc015b1ae9d08ab6eb42'
+            '39d8fe84e7262a11fb49700254fd54a9823ad25069f6cb9539d830c708d8864e'
+            '7dc09611d85955ced66dec3f9eb63a3396e59f0bd4f93e6338478a102b01f302'
+            '46c3437979fa9a836c5832f1d92c286b90950f7795903cc34051f48e7f0be403'
+            'df7bbf1363eec2af224251e77cd0a025003cd0ac751163a3e43cbe2bf52870d1'
+            'e4b5398d4e5fe81b0e57b2e5d3a7b1d9621c97d1b8ce40a2d5b169bd94e89397'
+            '8e999cabf53742fa818504a10f326e1275e23349f73267baba9058eda6add1ec'
+            'e8159c2a85ce43ea0d08ff4cf10525e5089db58a8c4f2bf9bfd0e368b4ecc099'
+            'f5cc878029b9d0469fa1db8a37a5f7e510871cc24ae6a24ecc011b5560f3bf9d'
+            '67785a6b1109f46203ff5f0169ed9d3f6118d72a3163e9141e10a24b1a10914f'
+            'aac5216b54d037f3cff3c76fa293c6afa08ed59e3e1865804f3af84569024e1e'
+            'ba9b05aac753a315c7ff373823cb752b535077209f4365a12a5e50d8742970f4'
+            '371a6a5b7ae241f77ef008984cf2b004d4d2aac373fe7dbe54ae9165c36f2c70'
+            '6efc50e2cf5e099f33634e702586e075fff4b34b9fc9f1a682b1c109e0343b85')
 depends=('java-runtime' 'java-openjfx')
 makedepends=('ant' 'git')
 optdepends=('beagle-lib')
+prepare(){
+    cd ${srcdir}/${pkgname}-${pkgver}
+    sed -i "s|2.7.1|2.7.2|" version.xml
+}
 build(){
     cd "$srcdir/BeastFX"
-    install -d release2/Linux/jrebin
+    install -Dm755 $srcdir/${pkgname}-${pkgver}/release/Linux/jrebin/* \
+        -t release2/Linux/jrebin
     ant linux -nouserlib -noinput \
         -Drelease_dir=release2 \
         -Dbeast2="../${pkgname}-${pkgver}" \
@@ -37,14 +52,24 @@ build(){
         -DopenjreLnx="/usr/lib/jvm/default/"
 }
 package() {
-    install -dm755 "$pkgdir"/usr/{bin,share/{beast2,applications}}
+    install -d "$pkgdir"/usr/share/beast2
+    install -d ${pkgdir}/usr/bin/$bin
     cd "$srcdir/BeastFX/release2/Linux/"
     cp -rf beast/* "${pkgdir}/usr/share/${pkgname}"
+
+    # correct excutable
+    rm -rf $pkgdir/usr/share/beast2/bin/*
+    for exe in {"beauti","densitree","logcombiner","treeannotator","beast2","loganalyser","applauncher"}
+    do
+        install -Dm755 $srcdir/${pkgname}-${exe} -t $pkgdir/usr/share/beast2/bin/
+    done
+    mv $pkgdir/usr/share/beast2/bin/${pkgname}-beast2  $pkgdir/usr/share/beast2/bin/${pkgname}
+
     for bin in $(ls $pkgdir/usr/share/beast2/bin)
-do
-    ln -s /usr/share/beast2/bin/$bin ${pkgdir}/usr/bin/$bin
-done
-    install -m 755 ${srcdir}/*.desktop ${pkgdir}/usr/share/applications
+    do
+        ln -s /usr/share/beast2/bin/$bin ${pkgdir}/usr/bin/$bin
+    done
+    install -Dm 755 ${srcdir}/*.desktop -t ${pkgdir}/usr/share/applications
 
     # clear files
     rm -rf $pkgdir/usr/share/beast2/jre
diff --git a/BioArchLinux/beast2/beast2-applauncher b/BioArchLinux/beast2/beast2-applauncher
new file mode 100755
index 0000000000..1b7a24288c
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-applauncher
@@ -0,0 +1,18 @@
+#!/bin/sh
+export JAVA_HOME=/usr/lib/jvm/default
+export BEAST=/usr/share/beast2
+
+BEAST_LIB="$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:$BEAGLE_LIB"
+
+# use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
+# this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
+if [ -n "$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 $*
+else
+  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher $*
+fi
diff --git a/BioArchLinux/beast2/applauncher.desktop b/BioArchLinux/beast2/beast2-applauncher.desktop
similarity index 87%
rename from BioArchLinux/beast2/applauncher.desktop
rename to BioArchLinux/beast2/beast2-applauncher.desktop
index 3036365cb7..66208e34e6 100755
--- a/BioArchLinux/beast2/applauncher.desktop
+++ b/BioArchLinux/beast2/beast2-applauncher.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast2/bin/applauncher
+Exec=beast2-applauncher
 Icon=/usr/share/beast2/images/beast.png
 MimeType=
 Name=applauncher
diff --git a/BioArchLinux/beast2/beast2-beast2 b/BioArchLinux/beast2/beast2-beast2
new file mode 100755
index 0000000000..543775a333
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-beast2
@@ -0,0 +1,12 @@
+#!/bin/sh
+export JAVA_HOME=/usr/lib/jvm/default
+export BEAST=/usr/share/beast2
+
+BEAST_LIB="$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:$BEAGLE_LIB"
+
+"$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 $*
diff --git a/BioArchLinux/beast2/beast2-beauti b/BioArchLinux/beast2/beast2-beauti
new file mode 100755
index 0000000000..6d24621260
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-beauti
@@ -0,0 +1,12 @@
+#!/bin/sh
+export JAVA_HOME=/usr/lib/jvm/default
+export BEAST=/usr/share/beast2
+
+BEAST_LIB="$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:$BEAGLE_LIB"
+
+"$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 $*
diff --git a/BioArchLinux/beast2/beast2-densitree b/BioArchLinux/beast2/beast2-densitree
new file mode 100755
index 0000000000..2bdf76f791
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-densitree
@@ -0,0 +1,12 @@
+#!/bin/sh
+export JAVA_HOME=/usr/lib/jvm/default
+export BEAST=/usr/share/beast2
+
+BEAST_LIB="$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:$BEAGLE_LIB"
+
+"$JAVA" -Xms256m -Xmx8g -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/DensiTree.jar:$BEAST/DensiTree.app/Contents/Resources/Java/DensiTree.jar" viz.DensiTree $*
diff --git a/BioArchLinux/beast2/beast2-loganalyser b/BioArchLinux/beast2/beast2-loganalyser
new file mode 100755
index 0000000000..21cc2c9dfa
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-loganalyser
@@ -0,0 +1,16 @@
+#!/bin/sh
+export JAVA_HOME=/usr/lib/jvm/default
+export BEAST=/usr/share/beast2
+
+BEAST_LIB="$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:$BEAGLE_LIB"
+
+# use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
+# this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
+if [ -n "$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 $*
+else
+  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
+fi
diff --git a/BioArchLinux/beast2/beast2-logcombiner b/BioArchLinux/beast2/beast2-logcombiner
new file mode 100755
index 0000000000..543302c2c0
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-logcombiner
@@ -0,0 +1,12 @@
+#!/bin/sh
+export JAVA_HOME=/usr/lib/jvm/default
+export BEAST=/usr/share/beast2
+
+BEAST_LIB="$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:$BEAGLE_LIB"
+
+"$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 $*
diff --git a/BioArchLinux/beast2/beast2-packagemanager b/BioArchLinux/beast2/beast2-packagemanager
new file mode 100755
index 0000000000..0c9113e2e2
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-packagemanager
@@ -0,0 +1,11 @@
+#!/bin/sh
+export JAVA_HOME=/usr/lib/jvm/default
+export BEAST=/usr/share/beast2
+
+BEAST_LIB="$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:$BEAGLE_LIB"
+"$JAVA" -Xms256m -Xmx8g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.pkgmgmt.PackageManager $*
diff --git a/BioArchLinux/beast2/beast2-treeannotator b/BioArchLinux/beast2/beast2-treeannotator
new file mode 100755
index 0000000000..dd2d6f638c
--- /dev/null
+++ b/BioArchLinux/beast2/beast2-treeannotator
@@ -0,0 +1,11 @@
+#!/bin/sh
+export JAVA_HOME=/usr/lib/jvm/default
+export BEAST=/usr/share/beast2
+
+BEAST_LIB="$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:$BEAGLE_LIB"
+"$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 $*
diff --git a/BioArchLinux/beast2/beast2.desktop b/BioArchLinux/beast2/beast2.desktop
index 6fd3ccea6a..bbdac0c438 100755
--- a/BioArchLinux/beast2/beast2.desktop
+++ b/BioArchLinux/beast2/beast2.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast2/bin/beast
+Exec=beast2
 Icon=/usr/share/beast2/images/beast.png
 MimeType=
 Name=beast2
diff --git a/BioArchLinux/beast2/beauti.desktop b/BioArchLinux/beast2/beauti.desktop
index 714a5b21c8..85585181d8 100755
--- a/BioArchLinux/beast2/beauti.desktop
+++ b/BioArchLinux/beast2/beauti.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast2/bin/beauti
+Exec=beast2-beauti
 Icon=/usr/share/beast2/images/beauti.png
 MimeType=
 Name=beauti
diff --git a/BioArchLinux/beast2/densitree.desktop b/BioArchLinux/beast2/densitree.desktop
index 88cdc3b8e0..22df35307b 100755
--- a/BioArchLinux/beast2/densitree.desktop
+++ b/BioArchLinux/beast2/densitree.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast2/bin/densitree
+Exec=beast2-densitree
 GenericName=
 GenericName[zh]=
 Icon=/usr/share/beast2/images/DensiTree.png
diff --git a/BioArchLinux/beast2/loganalyser.desktop b/BioArchLinux/beast2/loganalyser.desktop
index 452eb1e215..025b14b06f 100755
--- a/BioArchLinux/beast2/loganalyser.desktop
+++ b/BioArchLinux/beast2/loganalyser.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast2/bin/loganalyser
+Exec=beast2-loganalyser
 Icon=/usr/share/beast2/images/beast.png
 MimeType=
 Name=loganalyser
diff --git a/BioArchLinux/beast2/logcombiner.desktop b/BioArchLinux/beast2/logcombiner.desktop
index 06bcc6f758..67f0159b1a 100755
--- a/BioArchLinux/beast2/logcombiner.desktop
+++ b/BioArchLinux/beast2/logcombiner.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast2/bin/logcombiner
+Exec=beast2-logcombiner
 Icon=/usr/share/beast2/images/beast.png
 MimeType=
 Name=logcombiner
diff --git a/BioArchLinux/beast2/treeannotator.desktop b/BioArchLinux/beast2/treeannotator.desktop
index 963a448e10..6f7d2cdaf7 100755
--- a/BioArchLinux/beast2/treeannotator.desktop
+++ b/BioArchLinux/beast2/treeannotator.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast2/bin/treeannotator
+Exec=beast2-treeannotator
 GenericName=
 GenericName[zh]=
 Icon=/usr/share/beast2/images/beast.png