beast2: fix some executables

2025-03-10 12:02:42 +00:00 · 2022-11-02 10:39:48 +08:00 · 2022-11-02 10:39:48 +08:00 · d269b70c22
commit d269b70c22
parent 12648dd48f
10 changed files with 85 additions and 40 deletions
--- a/BioArchLinux/beast2/PKGBUILD
+++ b/BioArchLinux/beast2/PKGBUILD
@ -6,19 +6,18 @@ pkgname=beast2
 pkgver=2.7.2
 pkgrel=2
 pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees. https://doi.org/10.1371/journal.pcbi.1003537"
-arch=('x86_64')
+arch=('any')
 url="http://www.beast2.org/"
 license=('LGPL')
 source=("${pkgname}-${pkgver}.tar.gz::https://github.com/CompEvol/beast2/archive/refs/tags/${pkgver}.tar.gz"
-"git+https://github.com/CompEvol/BeastFX.git#commit=e6c9fdb2"
- "beauti.desktop" "densitree.desktop" "logcombiner.desktop" "treeannotator.desktop" "beast2.desktop"
- "loganalyser.desktop" "${pkgname}-applauncher.desktop"
- # executable
- "${pkgname}-beauti" "${pkgname}-densitree" "${pkgname}-logcombiner" "${pkgname}-treeannotator" "${pkgname}-beast2"
- "${pkgname}-loganalyser" "${pkgname}-applauncher" "${pkgname}-packagemanager" "${pkgname}-environment"
+"BeastFX-${pkgver}.tar.gz::https://github.com/CompEvol/BeastFX/archive/refs/tags/v${pkgver}.tar.gz"
+# desktop
+{beauti,densitree,logcombiner,treeannotator,beast2,loganalyser,${pkgname}-applauncher}.desktop
+# excutables
+${pkgname}-{beauti,densitree,logcombiner,treeannotator,beast2,loganalyser,applauncher,packagemanager,environment}
 )
 sha256sums=('02f561f593adf54e512d34a9366dd9e4ed0b940cb4540d97a2b4e9b705f327a3'
-            'SKIP'
+            '1b4cca8ee299459469bfdf8a98b701ed5e47f0b015ef0e04964a195fd9fb74d5'
            'f35255c946a105a60e81fcf44ed3f5c28e6903f0e9cedc015b1ae9d08ab6eb42'
            '39d8fe84e7262a11fb49700254fd54a9823ad25069f6cb9539d830c708d8864e'
            '7dc09611d85955ced66dec3f9eb63a3396e59f0bd4f93e6338478a102b01f302'
@ -26,15 +25,15 @@ sha256sums=('02f561f593adf54e512d34a9366dd9e4ed0b940cb4540d97a2b4e9b705f327a3'
            'df7bbf1363eec2af224251e77cd0a025003cd0ac751163a3e43cbe2bf52870d1'
            'e4b5398d4e5fe81b0e57b2e5d3a7b1d9621c97d1b8ce40a2d5b169bd94e89397'
            '8e999cabf53742fa818504a10f326e1275e23349f73267baba9058eda6add1ec'
-            '6b935c9cd9eb7c901c2225083b92b410144eb67637443f54ba4bc99f1cd6bed1'
-            'ddcbeb065e1c9a1b0f745bb9df3dd2286bf5a3770f12b545962c5da33ccc3653'
-            'e9c61fd9798188e2153bfda533f7fbd4ae830cc6defe17847cbddf422873d054'
-            'e0b1931c484773b707b924b6014ee6e13b94abc47d37ccbf7b8d8af3befe4399'
-            'a6931ebff2b3f0cd8b8f99446ee0f93506cfe81fe8d254bd3f22a4e074a79588'
-            '34a6d929e0fc4d3e8d6bc68e6932a740c5193e37c321c231396168d7f4fc3a0e'
-            '3f2e227d433cdfdebe348eb3233b2b65497d8056a302fc95ecb1f2dbed7e1e77'
-            'a11c0a012cf96807a6d385e4503d480bca11855eecaab3f205c40e85efa721e7'
-            '0aef5826ec5523354216bdc9fe1342ee0dc39bf6d9e65e2ea8c9caad9fb5d843')
+            '102d9c9db73968dab199f88480af13746ce61974db2d22761308f6f38d7f7ee4'
+            '7c32c0c3c5ea9a429d9a9b52f4c9333a6134fe0e218d16eaf14fb4aa0eba8f3e'
+            '913b2ec3fcb7a0bbd6d6632abb00c016fd1ec53b9fc840da2afcf19cf3607c6c'
+            '66da5c58a820a6bf1da7508b3084e9cb245e4311882cec80ac7f0ba41c4ce575'
+            '35842165da98c57f40c490d7eb8a31f189d8f9099268892355d261d712910747'
+            'ca7447eba08526cd607bd566a7f826d068cb35fc18c1be7429a10c03a50b0e4f'
+            '337159e676c057af33fdafef8d64fb47e5a78d9130b7d4a8d5dd5c8d1bb8d35f'
+            '9ca416360e1697768aa5b9cad2cae13b2d9077dd2386d0950466bad6d5cccf60'
+            '7b6c125b3dbe7f65cd4903ebca6106893c808f2b444c29aba082f9a66c7ac6af')
 depends=('java-runtime' 'java-openjfx')
 makedepends=('ant' 'git')
 optdepends=('beagle-lib')
@ -42,10 +41,9 @@ 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"
+    cd "$srcdir/BeastFX-${pkgver}"
    install -Dm755 $srcdir/${pkgname}-${pkgver}/release/Linux/jrebin/* \
        -t release2/Linux/jrebin
    ant linux -nouserlib -noinput \
@ -54,22 +52,26 @@ build(){
        -Dbeast2path="../${pkgname}-${pkgver}" \
        -lib "/usr/lib/jvm/default-runtime/lib" \
        -Dcommon_dir="../${pkgname}-${pkgver}/release/common/" \
-        -DopenjreLnx="/usr/lib/jvm/default/"
+        -DopenjreLnx="/usr/lib/jvm/default/" \
+        -DBEASTappName="BeastFX-${pkgver}" \
+        -DBeastFX="BeastFX-${pkgver}"
 }
 package() {
    install -d "$pkgdir"/usr/share/beast2
    install -d ${pkgdir}/usr/bin/$bin
-    cd "$srcdir/BeastFX/release2/Linux/"
+    cd "$srcdir/BeastFX-${pkgver}/release2/Linux/"
    cp -rf beast/* "${pkgdir}/usr/share/${pkgname}"

    # shipped modules
-    for module in {beastfx,beast,beagle}
+    for module in {beastfx,beast}
    do
        install -d "${pkgdir}/usr/share/${pkgname}/lib/${module}"
    done
-    cp -rf ${srcdir}/BeastFX/build/beastfx/* "${pkgdir}/usr/share/${pkgname}/lib/beastfx"
+    cp -rf ${srcdir}/BeastFX-${pkgver}/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"
+
+    # shipped library
+    install -Dm644 ${srcdir}/${pkgname}-${pkgver}/lib/*.jar -t  "${pkgdir}/usr/share/${pkgname}/lib"

    # correct excutable
    rm -rf $pkgdir/usr/share/beast2/bin/*
--- a/BioArchLinux/beast2/beast2-applauncher
+++ b/BioArchLinux/beast2/beast2-applauncher
@ -3,16 +3,25 @@ self_path=$(realpath $0)
 environment_file=$(dirname $self_path)/beast2-environment
 source $environment_file

+extra_jfx_modules=(
+  web
+  media
+  swing
+)
+
+EXTRA_JFX_MODULES=$(printf "javafx.%s," "${extra_jfx_modules[@]}" |sed 's/,*$//g')
+export JFX_MODULES="${JFX_MODULES},$EXTRA_JFX_MODULES"
+
 # use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations
 # this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en \
    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
-    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.launcher.AppLauncherLauncher $*
 else
  "$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 \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.launcher.AppLauncherLauncher $*
 fi
--- a/BioArchLinux/beast2/beast2-beast2
+++ b/BioArchLinux/beast2/beast2-beast2
@ -3,7 +3,8 @@ self_path=$(realpath $0)
 environment_file=$(dirname $self_path)/beast2-environment
 source $environment_file

+
 "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
-    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.launcher.BeastLauncher $*
--- a/BioArchLinux/beast2/beast2-beauti
+++ b/BioArchLinux/beast2/beast2-beauti
@ -3,7 +3,15 @@ self_path=$(realpath $0)
 environment_file=$(dirname $self_path)/beast2-environment
 source $environment_file

+extra_jfx_modules=(
+  web
+  media
+)
+
+EXTRA_JFX_MODULES=$(printf "javafx.%s," "${extra_jfx_modules[@]}" |sed 's/,*$//g')
+JFX_MODULES="${JFX_MODULES},$EXTRA_JFX_MODULES"
+
 "$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 \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.launcher.BeautiLauncher -capture $*
--- a/BioArchLinux/beast2/beast2-densitree
+++ b/BioArchLinux/beast2/beast2-densitree
@ -3,7 +3,8 @@ self_path=$(realpath $0)
 environment_file=$(dirname $self_path)/beast2-environment
 source $environment_file

+
 "$JAVA" -Xms256m -Xmx8g -Djava.library.path="$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 \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    viz.DensiTree $*
--- a/BioArchLinux/beast2/beast2-environment
+++ b/BioArchLinux/beast2/beast2-environment
@ -1,15 +1,38 @@
 #!/bin/sh

-# General environment for beast2
+# General environment for beast2, sourced by other beast2 excutables

 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 DEFAULT_CP="/usr/share/beast2/lib/beagle.jar"
 export BEAST_LIB="$BEAST/lib"
-export DEFAULT_CP="/usr/share/beast2/lib"
-
 export JAVA="$JAVA_HOME"/bin/java
+JFX="$JAVA_HOME/lib"
+export CLASS_PATH="/usr/share/beast2/lib:${JFX}"
+
+
+jfx_modules=(
+    controls
+    fxml
+    graphics
+    base
+    web
+    media
+    swing
+)
+for mod in ${jfx_modules[@]}
+do
+    JFX_LIBS="$JFX_LIBS:$JFX/javafx.${mod}.jar"
+done
+
+loaded_jfx_modules=(
+  controls
+  fxml
+)
+JFX_MODULES=$(printf "javafx.%s," "${loaded_jfx_modules[@]}" |sed 's/,*$//g')
+
+export JFX_LIBS
+export JFX_MODULES

 # use BEAGLE_LIB if the BEAGLE library is not in a standard location
 export BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
--- a/BioArchLinux/beast2/beast2-loganalyser
+++ b/BioArchLinux/beast2/beast2-loganalyser
@ -8,11 +8,11 @@ source $environment_file
 if [ -n "$BEAST_EXTRA_LIBS" ]; then
  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en \
    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
-    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
 else
  "$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 \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.launcher.AppLauncherLauncher LogAnalyser $*
 fi
--- a/BioArchLinux/beast2/beast2-logcombiner
+++ b/BioArchLinux/beast2/beast2-logcombiner
@ -5,5 +5,5 @@ source $environment_file

 "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
-    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.launcher.LogCombinerLauncher $*
--- a/BioArchLinux/beast2/beast2-packagemanager
+++ b/BioArchLinux/beast2/beast2-packagemanager
@ -3,7 +3,8 @@ self_path=$(realpath $0)
 environment_file=$(dirname $self_path)/beast2-environment
 source $environment_file

+
 "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
-    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.PackageManager $*
--- a/BioArchLinux/beast2/beast2-treeannotator
+++ b/BioArchLinux/beast2/beast2-treeannotator
@ -5,5 +5,5 @@ source $environment_file

 "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx8g -Djava.library.path=$LD_LIBRARY_PATH -Duser.language=en \
    -cp $DEFAULT_CP:$BEAST_LIB/launcher.jar \
-    --module-path $JFX_LIBS --add-modules javafx.controls,javafx.fxml \
+    --module-path $JFX_LIBS --add-modules "$JFX_MODULES" \
    beast.pkgmgmt.launcher.TreeAnnotatorLauncher $*