PKGBUILD for augustus

PKGBUILD

# Maintainer: Michael Schubert <mschu.dev at gmail>
# Contributor: sukanka <su975853527 at gmail>
pkgname=augustus
_pkgname=Augustus
pkgver=3.5.0
pkgrel=1
pkgdesc="A eucaryotic 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}/opt/augustus install

  # fix broken links
  for bin in {augustus,etraining,prepareAlign,fastBlockSearch}
  do
    ln -sf /opt/augustus/bin/${bin} "$pkgdir"/usr/bin/${bin}
  done
  rm "$pkgdir"/usr/bin/{load2db,getSeq}

  # link utils, note: load2db,getSeq are prefixed with augustus in /usr/bin
  for bin in {aln2wig,bam2hints,bam2wig,compileSpliceCands,filterBam,homGeneMapping,joingenes,load2sqlitedb,pp_simScore,load2db,getSeq}
  do
    ln -sf /opt/augustus/bin/${bin} "$pkgdir"/usr/bin/augustus-${bin}
  done

  install -Dm644 src/LICENSE.TXT "$pkgdir"/usr/share/licenses/augustus/LICENSE
}

hi, thanks a lot for your efforts. this PKGBUILD was able to compile the package successfully. however, while integrating with braker pipeline following options creates issues

# link utils, note: load2db,getSeq are prefixed with augustus in /usr/bin
for bin in {aln2wig,bam2hints,bam2wig,compileSpliceCands,filterBam,homGeneMapping,joingenes,load2sqlitedb,pp_simScore,load2db,getSeq}
do
  ln -sf /opt/augustus/bin/${bin} "$pkgdir"/usr/bin/augustus-${bin}
done

braker pipeline expects these tools without "augustus-" prefix. even if i alias them to upstream names in ~/.bashrc the braker scripts wouldn't work. right now i have to manually edit every script in braker pipeline to replace all instances aforementioned utils with "augustus-" prefix.

Is it possible to build packages without this?

hi, thanks a lot for your efforts. this PKGBUILD was able to compile the package successfully. however, while integrating with braker pipeline following options creates issues

# link utils, note: load2db,getSeq are prefixed with augustus in /usr/bin
for bin in {aln2wig,bam2hints,bam2wig,compileSpliceCands,filterBam,homGeneMapping,joingenes,load2sqlitedb,pp_simScore,load2db,getSeq}
do
  ln -sf /opt/augustus/bin/${bin} "$pkgdir"/usr/bin/augustus-${bin}
done

braker pipeline expects these tools without "augustus-" prefix. even if i alias them to upstream names in ~/.bashrc the braker scripts wouldn't work. right now i have to manually edit every script in braker pipeline to replace all instances aforementioned utils with "augustus-" prefix.

Is it possible to build packages without this?

Surely you can. I added this prefix as the names like load2db,getSeq are too general.

You can remove the prefix in pkgbuild, but I recommend make scripts in braker use /opt/augustus/bin/ instead of /usr/bin so you can call the excutables directly without prefix.

A workaround is to add

export PATH=/opt/augustus/bin:$PATH

in the scripts.