viennarna: version 2.5.1

BioArchLinux/viennarna/PKGBUILD

@@ -0,0 +1,122 @@
+# import from AUR: bipin kumar <bipin@ccmb.res.in
+# Maintainer: Ronny Lorenz <ronny at tbi dot univie dot ac dot at>
+
+pkgbase=viennarna
+pkgname=('viennarna' 'python-rna' 'perl-rna')
+pkgver=2.5.1
+pkgrel=1
+pkgdesc="RNA Secondary Structure Prediction and Comparison"
+arch=('x86_64' 'i686')
+license=('Custom')
+url="http://www.tbi.univie.ac.at/RNA"
+groups=('viennarna-package')
+makedepends=( 'perl'
+              'python'
+              'libtool'
+              'check'
+              'mpfr'
+              'gsl')
+source=(http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${pkgver}.tar.gz)
+
+options=('staticlibs' '!strip')
+sha256sums=('05400437cf15595e10b1a25df6c9c48856f356130f9d1e380fa8866b6d27f457')
+
+prepare() {
+  cd "${srcdir}/ViennaRNA-${pkgver}"
+  ./configure \
+      --with-cluster \
+      --with-kinwalker \
+      --prefix=/usr \
+      --without-python2 \
+      INSTALLDIRS=vendor
+}
+
+build() {
+  cd "${srcdir}/ViennaRNA-${pkgver}"
+  make
+}
+
+check() {
+  cd "$srcdir/ViennaRNA-${pkgver}"
+  export LC_ALL=C
+  make check
+}
+
+package_viennarna() {
+  depends=('perl'
+           'r'
+           'python'
+           'mpfr'
+           'gsl')
+  optdepends=('gri: create 2D plots of secondary structure landscape with RNA2Dfold')
+  provides=('Kinfold=1.4'
+            'RNAforester=2.0'
+            'kinwalker=2.0'
+            "viennarna2=${pkgver}"
+            "libRNA=${pkgver}")
+  conflict=('kinwalker')
+
+  cd "${srcdir}/ViennaRNA-${pkgver}"
+
+  # install executables
+  cd src/bin/
+  make DESTDIR="${pkgdir}" install
+  cd ../Kinfold
+  make DESTDIR="${pkgdir}" install
+  cd ../RNAforester
+  install -Dm755 src/RNAforester "${pkgdir}/usr/bin/"
+  install -Dm644 man/RNAforester.1* "${pkgdir}/usr/share/man/man1/"
+  cd ../Utils
+  make DESTDIR="${pkgdir}" install
+  cd ../Cluster
+  make DESTDIR="${pkgdir}" install
+  cd ../Kinwalker
+  make DESTDIR="${pkgdir}" install
+  cd ../RNAlocmin
+  make DESTDIR="${pkgdir}" install
+  cd ../..
+
+  # install library and header files
+  cd src/ViennaRNA
+  make DESTDIR="${pkgdir}" install
+  cd ../..
+
+  # install manpages, documentation, examples, and misc files
+  cd man
+  make DESTDIR="${pkgdir}" install
+  cd ../doc
+  make DESTDIR="${pkgdir}" install
+  cd ../examples
+  make DESTDIR="${pkgdir}" install
+  cd ../misc
+  make DESTDIR="${pkgdir}" install
+  cd ..
+
+  # install pkg-config file
+  install -Dm644 RNAlib2.pc "$pkgdir/usr/lib/pkgconfig/RNAlib2.pc"
+
+  install -Dm644 COPYING "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+
+  # cleanup after dirty install ...
+  install -dm755 "$pkgdir"/usr/bin/vendor_perl
+  for perlscript in "$pkgdir"/usr/share/ViennaRNA/bin/*.pl ; do
+    mv "$perlscript" "$pkgdir/usr/bin/vendor_perl/"
+  done
+
+  # no need for that file it is outdated anyway
+  rm $pkgdir/usr/share/info/dir
+}
+
+package_python-rna() {
+  depends=('python' viennarna="${pkgver}")
+  cd "${srcdir}/ViennaRNA-${pkgver}"
+  cd interfaces/Python
+  make DESTDIR="${pkgdir}" install
+}
+
+package_perl-rna() {
+  depends=('perl' viennarna="${pkgver}")
+  cd "${srcdir}/ViennaRNA-${pkgver}"
+  cd interfaces/Perl
+  make DESTDIR="${pkgdir}" install
+}

BioArchLinux/viennarna/lilac.yaml

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+build_prefix: extra-x86_64
+maintainers:
+  - github: kbipinkumar
+    email: bipin@ccmb.res.in
+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: regex
+    regex: 'ViennaRNA-(\d+.\d+.\d+).tar.gz'
+    url: "http://www.tbi.univie.ac.at/RNA/packages/source/"