Merge pull request #96 from kbipinkumar/augustus

augustus: init

BioArchLinux/augustus/PKGBUILD

@@ -0,0 +1,39 @@
+# Maintainer: bipin kumar <bipin@ccmb.res.in>
+# Contributor: sukanka <su975853527 at gmail>
+pkgname=augustus
+_pkgname=Augustus
+pkgver=3.5.0
+pkgrel=1
+pkgdesc="A eukaryotic gene prediction program"
+arch=('i686' 'x86_64')
+url="http://augustus.gobics.de/"
+license=('custom:Artistic-2.0')
+depends=('bamtools'  'boost-libs' 'gsl' 'mysql++' 'sqlite' 'python' 'lpsolve' 'perl' 'htslib')
+makedepends=('boost' 'suitesparse' 'samtools' )
+source=($pkgname-$pkgver.tar.gz::https://github.com/Gaius-Augustus/Augustus/archive/v$pkgver.tar.gz)
+sha256sums=('5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686')
+
+prepare() {
+  cd $_pkgname-$pkgver
+  sed -i "s|/usr/local/bin|/usr/bin|" Makefile
+}
+
+build() {
+  cd $_pkgname-$pkgver
+  make SAMTOOLS=/usr/include/bam PREFIX="$pkgdir"/usr INSTALLDIR=${pkgdir}/opt/augustus
+}
+
+package() {
+  cd $_pkgname-$pkgver
+  install -d ${pkgdir}/usr/bin
+  make DESTDIR="$pkgdir" PREFIX="$pkgdir"/usr INSTALLDIR=${pkgdir}/usr/share/augustus install
+
+  # fix broken links
+  for bin in {augustus,etraining,prepareAlign,fastBlockSearch}
+  do
+    ln -sf /usr/share/augustus/bin/${bin} "$pkgdir"/usr/bin/${bin}
+  done
+  rm "$pkgdir"/usr/bin/{load2db,getSeq}
+
+  install -Dm644 src/LICENSE.TXT "$pkgdir"/usr/share/licenses/augustus/LICENSE
+}

BioArchLinux/augustus/lilac.yaml

@@ -0,0 +1,15 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: sukanka
+  email: su975853527@gmail.com
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_add_files('PKGBUILD')
+  git_commit()
+update_on:
+- source: github
+  github: Gaius-Augustus/Augustus
+  use_max_tag: true
+  prefix: 'v'