aliview: compile from source

1 files changed, 32 insertions, 22 deletions

diff --git a/PKGBUILD b/PKGBUILD
index aa33dc5de892..c5c49c1903f3 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,30 +1,40 @@
-# Maintainer: Fabio Zanini <fabio DOOT zanini AAT fastmail DOT fm>
+#Maintainer: Guoyi Zhang <myname at malacology dot net>
+#Contributor: Fabio Zanini <fabio DOOT zanini AAT fastmail DOOT fm>
+
 pkgname=aliview
-pkgver=1.27
-pkgrel=1
-pkgdesc="Software for aligning viewing and editing dna/aminoacid sequences."
+_pkgname=AliView
+pkgver=1.28
+pkgrel=2
+pkgdesc="Software for aligning viewing and editing dna/aminoacid sequences https://doi.org/10.1093/bioinformatics/btu531"
 arch=('any')
 url="http://www.ormbunkar.se/aliview/"
 license=('GPL')
-depends=('jre-openjdk')
-makedepends=()
-optdepends=()
-options=()
-install=
-changelog=
-source=("http://www.ormbunkar.se/${pkgname}/downloads/linux/linux-version-$pkgver/$pkgname.tgz")
-sha256sums=('c1ae05b949673540cf23cb6ebbcdc16689ae9c00ab528975f0665503440bdcd5')
-
-build() {
-	cd "$srcdir/aliview"
-	sed -i "s|/usr|$pkgdir/usr|" install.sh
-	sed -i 's|\[ -d ~/.local/share/applications \]|false|' install.sh
+depends=('java-runtime=8')
+makedepends=('maven' 'java-environment=8')
+source=("$pkgname.tar.gz::https://github.com/AliView/AliView/archive/refs/tags/v${pkgver}.tar.gz"
+	"$pkgname.patch::https://patch-diff.githubusercontent.com/raw/AliView/AliView/pull/123.patch"
+	"${pkgname}2.patch::https://github.com/AliView/AliView/pull/125.patch")
+sha256sums=('4af3459c6f29a002d8724c12b17d247673370c6fa10cb47adf55c18f57d9e139'
+            '16053c6d6cc9948aed439519d11230fa088a3e8850af63f840fab54f7fec0ed7'
+            '0452ddbbc2486c7632bf6f096215190a0bea2aae8c558da3fde8657a14f235bb')
+prepare(){
+  cd $srcdir/$_pkgname-$pkgver
+  patch -p1 < $srcdir/$pkgname.patch
+  patch -p1 < $srcdir/${pkgname}2.patch
 }
 
+build(){
+  cd $srcdir/$_pkgname-$pkgver
+  mvn package
+}
 
-package() {
-	cd "$srcdir/aliview"
-	mkdir -p $pkgdir/usr/bin
-	mkdir -p $pkgdir/usr/share
-	./install.sh
+package(){
+  cd $srcdir/$_pkgname-$pkgver
+  cd aliview-linux
+  install -Dm 755 $pkgname $pkgdir/usr/bin/$pkgname
+  install -Dm 644 $_pkgname.desktop $pkgdir/usr/share/applications/$_pkgname.desktop
+  install -Dm 755 aliicon_128x128.png $pkgdir/usr/share/$pkgname/aliicon_128x128.png
+  cd $srcdir/$_pkgname-$pkgver
+  cd target
+  install -Dm 755 $pkgname.jar $pkgdir/usr/share/$pkgname/$pkgname.jar
 }