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# Maintainer: Jens Staal <staal1978@gmail.com>
pkgname=ugene-git
pkgver=38.1.r431.gb644c7c177
pkgrel=1
pkgdesc="A free cross-platform genome analysis suite."
arch=('x86_64')
url="http://ugene.unipro.ru/"
license=('GPL')
depends=('libxtst' 'glu' 'qt5-webkit' 'qt5-websockets' 'qt5-svg' 'qt5-script' 'desktop-file-utils' 'qspec-git' 'opencl-driver')
makedepends=('git' 'opencl-headers')
#optdepends lists packages that otherwise are present in ugene-external-tools
optdepends=('cufflinks' 'bowtie' 'clustalw' 'phyml' 'blast+' 'clustal-omega' 'vcftools' 'mrbayes' 'bwa' 'bedtools'
'tcoffee' 'hmmer' 'snpeff' 'samtools' 'mafft' 'trimmomatic' 'stringtie' 'kraken' 'diamond-aligner'
'python2-cutadapt' 'python' 'java-runtime' 'bowtie2' 'tophat' 'fastqc')
#missing packages from ugene-external-tools: CAP3, bedgraph2BigWig wevote, metaphlan2, clark, spades, cistrome
provides=('ugene' 'ugene-bin')
conflicts=('ugene' 'ugene-bin')
source=('ugene::git+https://github.com/ugeneunipro/ugene.git')
sha256sums=('SKIP')
pkgver() {
cd "${srcdir}"/ugene
git describe --long --tags | sed 's/\([^-]*-g\)/r\1/; s/-/./g'
}
build() {
cd "${srcdir}"/ugene
#make sure that the wanted branch is active
git checkout master
CXXFLAGS="$CXXFLAGS -Wno-depreceated"
OPENCL_INC_PATH=/usr/include/CL
qmake CONFIG+=x64 INSTALL_PREFIX=${pkgdir}/opt/ugene UGENE_OPENCL_DETECTED=1 UGENE_USE_SYSTEM_SQLITE=1 UGENE_USE_BUNDLED_ZLIB=0 -r
make all
}
package() {
cd "${srcdir}"/ugene
make install
mkdir -p ${pkgdir}/usr/bin
ln -s /opt/ugene/ugene ${pkgdir}/usr/bin/ugene
mkdir -p ${pkgdir}/usr/share/applications
ln -s /opt/ugene/ugene.desktop ${pkgdir}/usr/share/applications/ugene.desktop
}
post_install() {
update-desktop-database -q
}
post_remove() {
update-desktop-database -q
}
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