diff options
Diffstat (limited to 'PKGBUILD')
| -rw-r--r-- | PKGBUILD | 54 |
1 files changed, 29 insertions, 25 deletions
@@ -1,37 +1,41 @@ -# Maintainer: Michael Schubert <mschu.dev at google mail> +# Maintainer: bipin kumar <kbipinkumar@pm.me> +# Contributor: sukanka <su975853527 at gmail> pkgname=augustus -pkgver=2.5.5 -pkgrel=1 -pkgdesc="A eucaryotic gene prediction program" +_pkgname=Augustus +pkgver=3.5.0 +pkgrel=5 +pkgdesc="A eukaryotic gene prediction program" arch=('i686' 'x86_64') url="http://augustus.gobics.de/" license=('custom:Artistic-2.0') -depends=('perl') -source=("http://augustus.gobics.de/binaries/$pkgname.$pkgver.tar.gz" - "http://augustus.gobics.de/binaries/LICENCE.TXT") -md5sums=('234adc8fe4c2ff0b70715fbf00173668' - '7e2216d2af60d1644c220cbad40b0e36') -options=(!strip) +depends=('bamtools' 'boost-libs' 'gsl' 'mysql++' 'sqlite' 'python' 'lpsolve' 'perl' 'htslib' 'python-pandas' 'python-numpy' 'python-biopython' 'mariadb-libs' 'gcc-libs' 'glibc' 'bash') +makedepends=('boost' 'suitesparse' 'samtools' ) +source=($pkgname-$pkgver.tar.gz::https://github.com/Gaius-Augustus/Augustus/archive/v$pkgver.tar.gz + "$pkgname.patch::https://github.com/Gaius-Augustus/Augustus/pull/395.patch") +sha256sums=('5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686' + 'f6676c6f9e5fade9adaf6a457fd87c9401a5ebc5f6aa4a87037990dd381afd1d') + +prepare() { + cd $_pkgname-$pkgver + patch -p1 < $srcdir/$pkgname.patch +} build() { - cd $pkgname.$pkgver - make all + cd $_pkgname-$pkgver + make SAMTOOLS=/usr/include/bam PREFIX="$pkgdir"/usr INSTALLDIR=${pkgdir}/usr/lib/augustus } package() { - cd $pkgname.$pkgver - - mkdir -p "$pkgdir/usr/share/augustus/scripts" - mkdir -p "$pkgdir/etc/"{augustus,profile.d} + cd $_pkgname-$pkgver + install -d ${pkgdir}/usr/bin + make DESTDIR="$pkgdir" PREFIX="$pkgdir"/usr INSTALLDIR=${pkgdir}/usr/lib/augustus install - cp -R bin "$pkgdir/usr/" - cp -R config "$pkgdir/etc/augustus/" - cp -R {docs,examples} "$pkgdir/usr/share/augustus/" - cp scripts/*.pl "$pkgdir/usr/share/augustus/scripts/" + # fix broken links + for bin in {augustus,etraining,prepareAlign,fastBlockSearch} + do + ln -sf /usr/lib/augustus/bin/${bin} "$pkgdir"/usr/bin/${bin} + done + rm "$pkgdir"/usr/bin/{load2db,getSeq} - echo export AUGUSTUS_CONFIG_PATH="/etc/augustus/config/" > "$pkgdir/etc/profile.d/augustus.sh" - chmod a+rx "$pkgdir/etc/profile.d/augustus.sh" - - install -Dm644 "$srcdir/LICENCE.TXT" "$pkgdir/usr/share/licenses/$pkgname/LICENSE" + install -Dm644 src/LICENSE.TXT "$pkgdir"/usr/share/licenses/augustus/LICENSE } - |