beast: build from source

BioArchLinux/beast/PKGBUILD

@@ -2,32 +2,67 @@
 # Contributor: Malacology <guoyizhang at malacology dot net>
 
 pkgname=beast
-pkgver=1.10.4
-pkgrel=12
-provides=("beast")
+pkgver=1.10.5pre_thorney_v0.1.2
+pkgrel=0
 pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
 arch=('x86_64')
 url="http://beast.community/"
-license=('LGPL-2.1 License')
-source=("https://github.com/beast-dev/beast-mcmc/releases/download/v${pkgver}/BEASTv${pkgver}.tgz" "beast_beast.desktop" "beauti_beast.desktop" "logcombiner_beast.desktop" "treeannotator_beast.desktop" "treestat_beast.desktop" "treestat.png")
-sha256sums=('be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8'
-            '4f3118c4ffc2added01200a42417cbdf0ca8549ab0b6fb5516b2eec2a2d77d14'
-            '8baa97527cf3af1c6f2b4cbe2825da83117b315222fb0b685e82a4b61bcaac3e'
-            'b420f1c78a2daf9b4a4d572a90228d83dcc9aba02690be8387c4e37d0f1ebe05'
-            '2317783703a95a98fc91a0a6d392bec1569e71ac62750d48a867e17c58b79586'
-            '32947f594b74e8aaf11813768dbf3be1eeec8153eb5d126da3800e8b34bc1396'
-            'aca5c3f88ea8624d94b9e6e0e8f4b41a1f981562ad33bee2f35cc15de84f9906')
-depends=('java-runtime')
-makedepends=('java-environment')
+license=('LGPL')
+source=("https://github.com/beast-dev/beast-mcmc/archive/refs/tags/v${pkgver}.tar.gz"
+	"beast.desktop"
+	"beast-beauti.desktop"
+	"beast-loganalyser.desktop"
+	"beast-logcombiner.desktop"
+	"beast-treeannotator.desktop"
+	"beast-treestat.desktop"
+	"fix_bin.patch")
+sha256sums=('7dac6881ca3cc53bb178388a068e735e3e11d1e1744bdcda1ac1699efe75f0e2'
+            'bd6f29c93a6ff8145de5af3137f976bfd84c4441bb3ee32778af4b0bcbcdb18b'
+            '1b84708063fd2ac39b8ff234c75d0fba2fc1737b82c926d9844db2694a21a91c'
+            '98b7b7cc4c2b744031b27d12bf737a6cb37a58e2e127539b53d49d4b7ada1524'
+            '3f25d0877ee9a4582e4bf7d8e7b964cbb2a5e5b642fc59097f5af18268b554ea'
+            'e9ff41cab265727bf781ad97cc014071a1d9b77890a44bc6005489a709ce542e'
+            '385c9078b0cac257b94a115ed000f71b9eb8b1d6c7edc1ba3e75a9724e11df05'
+            '086b899c6f4bfa43d4af61d497c0265d087e919de5723faa6b3e58ae48fb6813')
+depends=('java-runtime=8')
+makedepends=('java-environment' 'ant' 'cmake' 'beagle-lib')
 optdepends=('beagle-lib')
+build() {
+  cd $srcdir/$pkgname-mcmc-$pkgver 
+  ant dist
+  java -jar -Djava.library.path=/usr/lib build/dist/beast.jar -beagle_info
+}
+
 package() {
-    install -dm755 "$pkgdir"/usr/{bin,share/{applications,${pkgname}}}
-    sed -i 's/\/usr\/local\/lib/\/usr\/lib/g'  ${srcdir}/BEASTv${pkgver}/bin/beast
-    mv ${srcdir}/BEASTv${pkgver}/* ${pkgdir}/usr/share/beast/
-    for bin in $(ls $pkgdir/usr/share/beast/bin)
+  #install desktop
+  cd $srcdir/
+for des in $(ls *.desktop)
 do
-    ln -s /usr/share/beast2/bin/$bin ${pkgdir}/usr/bin/$bin
-done   
-    install -m 755 treestat.png ${pkgdir}/usr/share/beast/images/
-    install -m 755 *.desktop ${pkgdir}/usr/share/applications
-    }
+  install -Dm 755 $des $pkgdir/usr/share/applications/$des
+done
+
+  # install jar
+  cd $srcdir/$pkgname-mcmc-$pkgver
+  cd build/dist
+for jar in $(ls *.jar)
+do
+  install -Dm 755 $jar $pkgdir/usr/share/$pkgname/$jar
+done
+
+  # install bin
+  cd $srcdir/$pkgname-mcmc-$pkgver
+  cd release/Linux/scripts
+  patch -N -i $srcdir/fix_bin.patch
+for bin in $(ls)
+do
+  install -Dm 755 $bin $pkgdir/usr/bin/$bin
+done
+
+  # install icons
+  cd $srcdir/$pkgname-mcmc-$pkgver
+  cd release/common/icons
+for icon in $(ls *.png)
+do
+  install -Dm 644 $icon $pkgdir/usr/share/pixmaps/$icon
+done
+}

BioArchLinux/beast/beast-beauti.desktop

@@ -1,8 +1,8 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast/bin/beauti
-Icon=/usr/share/beast/images/beauti.png
+Exec=beauti
+Icon=beauti
 MimeType=
 Name=beauti
 ServiceTypes=

BioArchLinux/beast/beast-loganalyser.desktop

@@ -1,8 +1,8 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast/bin/logcombiner
-Icon=/usr/share/beast/images/utility.png
+Exec=loganalyser
+Icon=utility
 MimeType=
 Name=logcombiner
 Name[zh]=logcombiner

BioArchLinux/beast/beast-logcombiner.desktop

@@ -0,0 +1,16 @@
+[Desktop Entry]
+Categories=
+Encoding=UTF-8
+Exec=logcombiner
+Icon=utility
+MimeType=
+Name=logcombiner
+Name[zh]=logcombiner
+ServiceTypes=
+SwallowExec=
+SwallowTitle=
+Terminal=false
+TerminalOptions=
+Type=Application
+X-KDE-SubstituteUID=false
+X-KDE-Username=root

BioArchLinux/beast/beast-treeannotator.desktop

@@ -1,10 +1,10 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast/bin/treeannotator
+Exec=treeannotator
 GenericName=
 GenericName[zh]=
-Icon=/usr/share/beast/images/utility.png
+Icon=utility
 MimeType=
 Name=treeannotator
 ServiceTypes=

BioArchLinux/beast/beast-treestat.desktop

@@ -1,8 +1,8 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast/bin/treestat
-Icon=/usr/share/beast/images/treestat.png
+Exec=treestat
+Icon=TreeStat
 MimeType=
 Name=treestat
 Name[zh]=treestat

BioArchLinux/beast/beast.desktop

@@ -1,10 +1,10 @@
 [Desktop Entry]
 Categories=
 Encoding=UTF-8
-Exec=/usr/share/beast/bin/beast
+Exec=beast
 GenericName=
 GenericName[zh]=
-Icon=/usr/share/beast/images/beast.png
+Icon=beast
 MimeType=
 Name=beast
 Name[zh]=beast

BioArchLinux/beast/fix_bin.patch

@@ -0,0 +1,72 @@
+diff --git a/beast b/beast
+index 2607b4d..6d50a5f 100755
+--- a/beast
++++ b/beast
+@@ -22,5 +22,5 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+ 
+-BEAST_LIB="$BEAST/lib"
+-java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB:/usr/local/lib:$LD_LIBRARY_PATH" -cp "$BEAST_LIB/beast.jar" dr.app.beast.BeastMain $*
++BEAST_LIB="/usr/share/beast"
++java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB:/usr/lib:$LD_LIBRARY_PATH" -cp "$BEAST_LIB/beast.jar" dr.app.beast.BeastMain $*
+diff --git a/beauti b/beauti
+index d2cb818..bc57736 100755
+--- a/beauti
++++ b/beauti
+@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+ 
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
+ 
+diff --git a/loganalyser b/loganalyser
+index a728320..beaee3c 100755
+--- a/loganalyser
++++ b/loganalyser
+@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+ 
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast"
+ java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
+ 
+diff --git a/logcombiner b/logcombiner
+index 5fe9821..4fb5653 100755
+--- a/logcombiner
++++ b/logcombiner
+@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+ 
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast"
+ java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $*
+ 
+diff --git a/treeannotator b/treeannotator
+index c4eafc2..b9d065d 100755
+--- a/treeannotator
++++ b/treeannotator
+@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+ 
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast"
+ java -Xms64m -Xmx4096m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $*
+ 
+diff --git a/treestat b/treestat
+index d35bf6c..b584175 100755
+--- a/treestat
++++ b/treestat
+@@ -22,6 +22,6 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+ 
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="/usr/share/beast"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $*
+ 

BioArchLinux/beast/lilac.py

@@ -1,11 +0,0 @@
-#!/usr/bin/env python3
-
-from lilaclib import *
-
-def pre_build():
-  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
-
-def post_build():
-  git_add_files('PKGBUILD')
-  git_commit()
-  update_aur_repo()

BioArchLinux/beast/lilac.yaml

@@ -2,8 +2,18 @@ build_prefix: extra-x86_64
 maintainers:
   - github: starsareintherose
     email: kuoi@bioarchlinux.org
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_add_files('PKGBUILD')
+  git_commit()
+  update_aur_repo()
 update_on:
   - source: github
     github: beast-dev/beast-mcmc
     use_max_tag: true
-    include_regex: 'v(\d+.\d+.\d+)'
+    prefix: 'v'
+    include_regex: '[^v]+'
+repo_depends:
+  - beagle-lib