1 files changed, 63 insertions, 19 deletions
diff --git a/PKGBUILD b/PKGBUILD
index fcda9d3fb731..97f1cc5a214f 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,31 +1,75 @@
-# Maintainer: Clint Valentine <valentine.clint@gmail.com>
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Contributor: Clint Valentine <valentine.clint@gmail.com>
 
-pkgname='artemis'
+pkgname=artemis
+_pkgname=Artemis
 pkgver=18.2.0
-pkgrel=5
+pkgrel=6
 pkgdesc='A genome viewer and annotation tool that visualizes biological sequence features'
 arch=('x86_64')
 url=https://www.sanger.ac.uk/science/tools/"${pkgname}"
 license=('GPL2')
-depends=('java-runtime>=1.6')
-source=("${pkgname}"-"${pkgver}".tar.gz::https://github.com/sanger-pathogens/Artemis/releases/download/v${pkgver}/artemis-unix-release-${pkgver}.tar.gz)
-sha256sums=('06441e1abab139cb0a09d5844cb1b84ae727ace53a6c0efdd1eea8d8cfab8382')
-
+depends=('java-runtime')
+makedepends=('java-environment' 'maven')
+source=($pkgname-$pkgver.tar.gz::https://github.com/sanger-pathogens/Artemis/archive/refs/tags/v${pkgver}.tar.gz
+	act.desktop
+	artemis.desktop
+	bamview.desktop
+	dnaplotter.desktop)
+sha256sums=('842c055f5cce021adbaea4f076b2ea80335ab1e44fbaa34b2ab608df6314a18e'
+            'a7dda77f6518c98af6df88ba5d725f1b89d86aca125240f63a9c6e08afeb2a24'
+            'dea9a1cc47b110c4f6ebe17c1b698866082997ffd9e6008d89847ddf745a0789'
+            '3ca519b00ffac02d635a62884996ad5b8c4580d8ffe8fcd427ee4edee1562f00'
+            'ef584b45f9c92da15511779f20a1a1449915315066662e4c142ea4cd92dd717c')
+#prepare() {
+#scripts=('act' 'art' 'bamview' 'dnaplotter')
+#  cd $srcdir/$_pkgname-$pkgver
+#  patch -N -i $srcdir/fix_bin.patch
+#}
+build() {
+  cd $srcdir/$_pkgname-$pkgver
+  mvn validate
+  mvn package
+}
 package() {
-  cd "${srcdir}"/"${pkgname}"
+bina=('act' 'art' 'bamview' 'dnaplotter')
+scripts=('act' 'artemis' 'bamview' 'dnaplotter')
+
+  # desktop
+  cd $srcdir/
+  for des in ${scripts[@]}
+do
+  install -Dm 755 $des.desktop $pkgdir/usr/share/applications/$des.desktop
+done
+
+  # bin
+  cd $srcdir/$_pkgname-$pkgver
+  for bin in ${bina[@]}
+do
+  install -Dm 775 $bin $pkgdir/usr/share/$pkgname/$bin
+done
 
-  sed -i 's#ARTEMIS_HOME=`dirname "$PRG"`/.#ARTEMIS_HOME=/opt/artemis/#' art
-  sed -i 's#ACT_HOME=`dirname "$PRG"`/.#ACT_HOME=/opt/artemis/#' act
-  sed -i 's#ARTEMIS_HOME=`dirname "$PRG"`/.#ARTEMIS_HOME=/opt/artemis/#' dnaplotter
+  # jar
+  cd $srcdir/$_pkgname-$pkgver/target/jars
+  for jar in $(ls *.jar)
+do
+  install -Dm 755 $jar $pkgdir/usr/share/$pkgname/target/jars/$jar
+done
 
-  mkdir -p "${pkgdir}"/opt/"${pkgname}"/
-  cp -a * "${pkgdir}"/opt/"${pkgname}"/
+  # icons
+  cd $srcdir/$_pkgname-$pkgver/target/classes/images
+  for icn in ${scripts[@]}
+do
+  mv ${icn}_icon.png ${icn}.png
+  install -Dm 644 ${icn}.png $pkgdir/usr/share/pixmaps/${icn}.png
+done
 
-  scripts=('act' 'art' 'dnaplotter')
-  for script in "${scripts[@]}"; do
-    install -Dm775 "${script}" "${pkgdir}"/usr/bin/"${script}"
-    rm "${pkgdir}"/opt/"${pkgname}"/"${script}"
-  done
+  # link bin
+  cd $srcdir/$_pkgname-$pkgver
+  mkdir -p $pkgdir/usr/bin
+  for bin in ${bina[@]}
+do
+  ln -s /usr/share/$pkgname/$bin $pkgdir/usr/bin/$bin
+done
 
-  install -Dm644 README.md "${pkgdir}"/usr/share/doc/"${pkgname}"/README.md
 }