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# Maintainer: Bipin Kumar <bipin@ccmb.res.in>
pkgname=spaln
pkgver=2.4.13f
pkgrel=1
pkgdesc='Splicing-aware transcript (cDNA/EST or protein sequences) alignment to genomic DNA'
arch=('x86_64')
url='https://github.com/ogotoh/spaln'
license=('GPL3')
depends=('zlib' 'perl')
source=("${pkgname}-${pkgver}.tar.gz::https://github.com/ogotoh/spaln/archive/refs/tags/ver.${pkgver}.tar.gz"
"spaln.sh"
"spaln.csh"
"destdir.patch")
sha256sums=('024fdcf58e38373983092280a7e10ff9c7e246e7d2465c165e158512e686225e'
'16e205ed8baf72052d6bce8a758eaae73e29d2469bd6825c6374dc652a5c165c'
'8529a45783eee4f9e0c668e8ef670ab95cf02fb60059d5e442b0283d60a83e7c'
'b78d8bf6c79cee8aa0a06e5aa61098041d46a468275fda911883d356866f8a8f')
prepare() {
cp destdir.patch ${pkgname}-ver.${pkgver}/src
cp spaln.* ${pkgname}-ver.${pkgver}/src
cd ${pkgname}-ver.${pkgver}/src
# patch to enable support for GNU make's staged install process
patch -p1 < destdir.patch
CXX=g++ CFLAGS="-O2" ./configure --exec_prefix=/usr/bin --table_dir=/usr/share/spaln/table --alndbs_dir=/usr/share/spaln/seqdb --use_zlib=1
}
build() {
cd ${pkgname}-ver.${pkgver}/src
make
}
package() {
cd ${pkgname}-ver.${pkgver}/src
make DESTDIR=${pkgdir} install
# set paths to tables and alndbs
install -dm755 "${pkgdir}"/etc/profile.d/
install -Dm644 spaln.sh -t "${pkgdir}"/etc/profile.d/
install -Dm644 spaln.csh -t "${pkgdir}"/etc/profile.d/
}
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