fix: compile serveral

author: Kuoi 2023-04-28 23:58:24 +0800
committer: Kuoi 2023-04-28 23:58:24 +0800
commit: 24c6f8e8a7f76d6a551e86c7b5b5fbde36963248 (patch)
tree: 3329cd89fe08d35270fdc0e8767d456972ca326b
parent: 9623785b2859f77a036494314ccd60cb4e011ed1 (diff)
download: aur-24c6f8e8a7f76d6a551e86c7b5b5fbde36963248.tar.gz
2 files changed, 179 insertions, 60 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 6a29c3dc7e0e..da5e916bab97 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,6 @@
 pkgbase = beast
-	pkgdesc = Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214
-	pkgver = sars__cov__2__origins
-	pkgrel = 2
+	pkgver = 1.10.4
+	pkgrel = 0
 	url = http://beast.community/
 	arch = x86_64
 	license = LGPL
@@ -9,23 +8,25 @@ pkgbase = beast
 	makedepends = ant
 	makedepends = cmake
 	makedepends = beagle-lib
+	makedepends = gendesk
 	depends = java-runtime=8
-	optdepends = beagle-lib
-	source = https://github.com/beast-dev/beast-mcmc/archive/refs/tags/sars-cov-2-origins.tar.gz
-	source = beast.desktop
-	source = beast-beauti.desktop
-	source = beast-loganalyser.desktop
-	source = beast-logcombiner.desktop
-	source = beast-treeannotator.desktop
-	source = beast-treestat.desktop
-	source = fix_bin.patch
-	sha256sums = fab8750313b66844f4dd8dcacfa55913f30bb877bded87057ba347d38cc9dc75
-	sha256sums = fa9841f5005be6d743ad278b037de0eb329c642de62e4996cc1df31272ffa185
-	sha256sums = e3897ee92348b3e48010af739fcbf7fbb38bcc2c18e1ceb30cd147b3c7067b2d
-	sha256sums = dcf674ebe5f1b7b13e746441f7a28a9b0fa86c03f3bef27833c532f323cb6644
-	sha256sums = 75842d174f246c38dc4600357ef8b41f67e5f12cbd7dba779d224f99b531cb1d
-	sha256sums = 6e63a619a6fb3101606a85dbc352d579e343d167cf79be67ccf31ed1544d5fd2
-	sha256sums = 3a21774077658117f36bd289901ec1d560a66bbe435ba4ddbc1980c558fa7362
-	sha256sums = 086b899c6f4bfa43d4af61d497c0265d087e919de5723faa6b3e58ae48fb6813
+	source = https://github.com/beast-dev/beast-mcmc/archive/refs/tags/v1.10.4.tar.gz
+	source = beast.patch::https://patch-diff.githubusercontent.com/raw/beast-dev/beast-mcmc/pull/1149.patch
+	sha256sums = 6e28e2df680364867e088acd181877a5d6a1d664f70abc6eccc2ce3a34f3c54a
+	sha256sums = 2f65ebb8c45feed0b2969276c7caae147b83f4f1dd4fc5e1d705aada2c4163e1
 
 pkgname = beast
+	pkgdesc = Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214
+	optdepends = beagle-lib
+
+pkgname = beastgen
+	pkgdesc = Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214
+	optdepends = beagle-lib
+
+pkgname = coalgen
+	pkgdesc = BEAST Coalescent Tree Simulator https://doi.org/10.1186/1471-2148-7-214
+	optdepends = beagle-lib
+
+pkgname = phylogeography
+	pkgdesc = BEAST PhyloGeography https://doi.org/10.1186/1471-2148-7-214
+	optdepends = beagle-lib
diff --git a/PKGBUILD b/PKGBUILD
index 489bfc4fe13c..a65053b6c973 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,68 +1,186 @@
 # Maintainer: Malacology <guoyizhang at malacology dot net>
 # Contributor: Malacology <guoyizhang at malacology dot net>
-
-pkgname=beast
-pkgver=sars__cov__2__origins
-pkgrel=2
-pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
+basename=beast
+pkgname=('beast' 'beastgen' 'coalgen' 'phylogeography' )
+pkgver=1.10.4
+pkgrel=0
 arch=('x86_64')
 url="http://beast.community/"
 license=('LGPL')
-source=("https://github.com/beast-dev/beast-mcmc/archive/refs/tags/${pkgver//__/-}.tar.gz"
-	"beast.desktop"
-	"beast-beauti.desktop"
-	"beast-loganalyser.desktop"
-	"beast-logcombiner.desktop"
-	"beast-treeannotator.desktop"
-	"beast-treestat.desktop"
-	"fix_bin.patch")
-sha256sums=('fab8750313b66844f4dd8dcacfa55913f30bb877bded87057ba347d38cc9dc75'
-            'fa9841f5005be6d743ad278b037de0eb329c642de62e4996cc1df31272ffa185'
-            'e3897ee92348b3e48010af739fcbf7fbb38bcc2c18e1ceb30cd147b3c7067b2d'
-            'dcf674ebe5f1b7b13e746441f7a28a9b0fa86c03f3bef27833c532f323cb6644'
-            '75842d174f246c38dc4600357ef8b41f67e5f12cbd7dba779d224f99b531cb1d'
-            '6e63a619a6fb3101606a85dbc352d579e343d167cf79be67ccf31ed1544d5fd2'
-            '3a21774077658117f36bd289901ec1d560a66bbe435ba4ddbc1980c558fa7362'
-            '086b899c6f4bfa43d4af61d497c0265d087e919de5723faa6b3e58ae48fb6813')
+source=("https://github.com/beast-dev/beast-mcmc/archive/refs/tags/v${pkgver//__/-}.tar.gz"
+	"$basename.patch::https://patch-diff.githubusercontent.com/raw/beast-dev/beast-mcmc/pull/1149.patch")
+sha256sums=('6e28e2df680364867e088acd181877a5d6a1d664f70abc6eccc2ce3a34f3c54a'
+            '2f65ebb8c45feed0b2969276c7caae147b83f4f1dd4fc5e1d705aada2c4163e1')
 depends=('java-runtime=8')
-makedepends=('java-environment=8' 'ant' 'cmake' 'beagle-lib')
-optdepends=('beagle-lib')
+makedepends=('java-environment=8' 'ant' 'cmake' 'beagle-lib' 'gendesk')
+
+prepare(){
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  patch -p1 < $srcdir/$basename.patch
+}
+
 build() {
-  cd $srcdir/$pkgname-mcmc-${pkgver//__/-}
-  ant dist
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  ant linux
   java -jar -Djava.library.path=/usr/lib build/dist/beast.jar -beagle_info
+  cp -r build/dist dist_beast
+  ant -buildfile build_beastgen.xml package
+  cp -r dist dist_beastgen
+  ant -buildfile build_bss.xml linux
+  cp -r dist dist_pibuss
+  ant -buildfile build_coalsim.xml dist
+  cp -r dist dist_coalgen
+  ant -buildfile build_phylogeography.xml package
+  cp -r dist dist_phylogeography
+  ant -buildfile build_tempest.xml dist
+  cp -r dist dist_tempest
 }
 
-package() {
-  #install desktop
-  cd $srcdir/
-for des in $(ls *.desktop)
-do
-  install -Dm 755 $des $pkgdir/usr/share/applications/$des
-done
+package_beast() {
+  pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
+  optdepends=('beagle-lib')
 
   # install jar
-  cd $srcdir/$pkgname-mcmc-${pkgver//__/-}
-  cd build/dist
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  cd dist_beast
 for jar in $(ls *.jar)
 do
   install -Dm 755 $jar $pkgdir/usr/share/$pkgname/$jar
 done
 
-  # install bin
-  cd $srcdir/$pkgname-mcmc-${pkgver//__/-}
+  # install bin, desktop
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
   cd release/Linux/scripts
-  patch -N -i $srcdir/fix_bin.patch
+  sed -i "s@/usr/local/lib@/usr/lib@g" *
+  sed -i "s@\$BEAST/lib@/usr/share/beast@g" *
 for bin in $(ls)
 do
-  install -Dm 755 $bin $pkgdir/usr/bin/$bin
+  install -Dm 755 $bin $pkgdir/usr/bin/$pkgname-$bin
+  gendesk --pkgname "$bin" --pkgdesc "$pkgdesc" --exec="$pkgname-$bin" --icon="/usr/share/pixmaps/$bin.png"
+  install -Dm 755 $bin.desktop $pkgdir/usr/share/applications/$basename-$bin.desktop
 done
 
   # install icons
-  cd $srcdir/$pkgname-mcmc-${pkgver//__/-}
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
   cd release/common/icons
 for icon in $(ls *.png)
 do
-  install -Dm 644 $icon $pkgdir/usr/share/pixmaps/$icon
+  install -Dm 644 $icon $pkgdir/usr/share/pixmaps/${icon,,}
 done
+
+  # ln icons
+for png in loganalyser logcombiner treeannotator
+do
+  ln -s /usr/share/pixmaps/utility.png $pkgdir/usr/share/pixmaps/$png.png
+done 
 }
+
+package_beastgen(){
+  pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
+  optdepends=('beagle-lib')
+  
+  # install jar
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  cd dist_beastgen
+  install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
+
+  # install bin
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  cd release_beastgen/common/bin/
+  sed -i "s@\$BEASTGEN/lib@/usr/share/beastgen@g" beastgen
+  install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
+}
+
+#package_pibuss(){
+#  pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. https://doi.org/10.1186/1471-2105-15-133"
+#  optdepends=('beagle-lib')
+#  # install jar
+#  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+#  cd dist_pibuss
+#  install -Dm 755 buss.jar $pkgdir/usr/share/$pkgname/buss.jar
+#
+#  # install bin
+#  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+#  cd release_pibuss/Linux/scripts/
+#  sed -i "s@/usr/local/lib@/usr/lib@g" pibuss
+#  sed -i "s@\$PIBUSS/lib@/usr/share/pibuss@g" pibuss
+#  install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
+#
+#  # install icons
+#  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+#  cd release_pibuss/Linux/icons
+#  install -Dm 644 $pkgname.png  $pkgdir/usr/share/pixmaps/$pkgname.png
+#
+#  # install pibuss.desktop
+#  gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.png"
+#  install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
+#}
+
+package_coalgen(){
+  pkgdesc="BEAST Coalescent Tree Simulator https://doi.org/10.1186/1471-2148-7-214"
+  optdepends=('beagle-lib')
+  
+  # install jar
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  cd dist_coalgen
+  install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
+
+  # install bin
+  echo "COALGEN_LIB=/usr/share/coalgen" >> $pkgname
+  echo "java -Xms64m -Xmx1024m -Djava.library.path=\"\$COALGEN_LIB:/usr/lib\" -jar \$COALGEN_LIB/coalgen.jar \$*" >> $pkgname
+  chmod +x $pkgname
+  install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
+
+  # icon
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  install -Dm 644 src/dr/app/coalgen/images/CoalGen.png $pkgdir/usr/share/pixmaps/$pkgname.png
+
+  # desktop
+  gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.png"
+  install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
+}
+
+
+package_phylogeography(){
+  pkgdesc="BEAST PhyloGeography https://doi.org/10.1186/1471-2148-7-214"
+  optdepends=('beagle-lib')
+
+  # install jar
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  cd dist_$pkgname
+  install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
+
+  # install bin
+  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+  cd release_phylogeography/common/bin/
+for bin in continuous_tree_to_kml discrete_rate_prior_generator discrete_tree_to_kml rate_indicator_bf timeslicer
+do
+  sed -i "s@\$PHYLOGEOGRAPHY/lib@/usr/share/phylogeography@g" $bin
+  install -Dm 755 $bin $pkgdir/usr/bin/$bin
+done
+
+}
+
+#package_tempest(){
+#  pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. https://doi.org/10.1093/ve/vew007"
+#
+#  # install jar
+#  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+#  cd dist_$pkgname
+#  install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
+#
+#  # install bin
+#  echo "TEMPEST_LIB=/usr/share/tempest" >> $pkgname
+#  echo "java -Xms64m -Xmx1024m -Djava.library.path=\"\$TEMPEST_LIB:/usr/lib\" -jar \$TEMPEST_LIB/tempest.jar \$*" >> $pkgname
+#  chmod +x $pkgname
+#  install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
+#
+#  # install ico
+#  cd $srcdir/$basename-mcmc-${pkgver//__/-}
+#  cd release_$pkgname/Windows/icons
+#  install -Dm 644 TempEst.ico  $pkgdir/usr/share/pixmaps/$pkgname.ico
+#
+#  # desktop
+#  gendesk --pkgname "$pkgname" --pkgdesc "$pkgdesc" --exec="$pkgname" --icon="/usr/share/pixmaps/$pkgname.ico"
+#  install -Dm 755 $pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
+#}
author	Kuoi	2023-04-28 23:58:24 +0800
committer	Kuoi	2023-04-28 23:58:24 +0800
commit	24c6f8e8a7f76d6a551e86c7b5b5fbde36963248 (patch)
tree	3329cd89fe08d35270fdc0e8767d456972ca326b
parent	9623785b2859f77a036494314ccd60cb4e011ed1 (diff)
download	aur-24c6f8e8a7f76d6a551e86c7b5b5fbde36963248.tar.gz