jmodeltest: rm extra files

BioArchLinux/jmodeltest/PKGBUILD

@@ -2,24 +2,37 @@
 # Contributor: Malacology <guoyizhang at malacology dot com>
 
 pkgname=jmodeltest
+_pkgname=jmodeltest2
 pkgver=2.1.10r20160303
-_pkgver=2.1.10
-pkgrel=5
+pkgrel=6
 pkgdesc="Phylogenetic Model Averaging, more models, new heuristics and high-performance computing. https://doi.org/10.1093/molbev/msn083"
 arch=('x86_64')
 provides=("jmodeltest")
 url="https://github.com/ddarriba/jmodeltest2"
-license=('GPL-3.0 License')
-source=("https://github.com/ddarriba/jmodeltest2/files/157117/jmodeltest-${_pkgver}.tar.gz" "jmodeltest.desktop")
-sha256sums=('9039f1a00e730b38e607126703606f8c2ff8309dd82955ce52ccc1ae2889d06d'
+license=('GPL3')
+source=("$url/archive/refs/tags/v$pkgver.zip" "jmodeltest.desktop")
+sha256sums=('62415b31f218c2f194d6a4a3ba4cccbfd0fc6073e5f11bc74680e1d9b2af86c5'
             'b35c9b5041ca7b9e0e96f29a958da356b9e5149d8ee581ff7c5c83adbcd6706f')
-depends=(
-	'java-runtime'
-)
-package() {
-    install -dm 755 $pkgdir/usr/share/{applications,${pkgname}}
-    
-    mv ${srcdir}/jmodeltest-${_pkgver}/* "${pkgdir}/usr/share/jmodeltest"
- 
-    install -m 755 ${srcdir}/jmodeltest.desktop ${pkgdir}/usr/share/applications/jmodeltest.desktop
+depends=('java-runtime')
+makedepends=('ant')
+optdepends=('phyml' 'phyml-mpi')
+install="$pkgname.install"
+build(){
+  cd $_pkgname-$pkgver
+  ant
+}
+package() {
+  install -dm 755 $pkgdir/usr/share/{applications,${pkgname}}
+  cd $_pkgname-$pkgver/dist
+  cp conf/jmodeltest.conf conf/jmodeltest.conf.mpi
+  sed -i 's@exe/phyml@exe/phyml-mpi@g' conf/jmodeltest.conf.mpi
+for dir in conf lib resources exe
+do	
+    mv ${srcdir}/jmodeltest2-${pkgver}/dist/$dir "${pkgdir}/usr/share/jmodeltest"
+done
+  mkdir -p $pkgdir/usr/share/$pkgname/exe/phyml-mpi
+  ln -s /usr/bin/phyml $pkgdir/usr/share/$pkgname/exe/phyml/PhyML_3.0_linux64
+  ln -s /usr/bin/phyml-mpi  $pkgdir/usr/share/$pkgname/exe/phyml-mpi/PhyML_3.0_linux64
+  install -Dm 755 $srcdir/$_pkgname-$pkgver/dist/jModelTest.jar $pkgdir/usr/share/$pkgname/jModelTest.jar
+  install -Dm 755 ${srcdir}/jmodeltest.desktop ${pkgdir}/usr/share/applications/jmodeltest.desktop
 }

BioArchLinux/jmodeltest/jmodeltest.install

@@ -0,0 +1,13 @@
+post_install() {
+    echo ""
+    echo "==> You must install phyml or phyml-mpi"
+    echo ""
+    echo "==> Default setting is phyml"
+    echo ""
+    echo "==> To use phyml-mpi"
+    echo ""
+    echo "==> cp /usr/share/jmodeltest/conf/jmodeltest.conf /usr/share/jmodeltest/conf/jmodeltest.conf.bak"
+    echo ""
+    echo "==> cp /usr/share/jmodeltest/conf/jmodeltest.conf.mpi cp /usr/share/jmodeltest/conf/jmodeltest.conf"
+    echo ""
+}