Arch Linux

drno

Member

Registered: 2017-11-11

Posts: 6

PKGBUILD for ncbi-igblast-1.7.0

I wrote a PKGBUILD for ncbi-igblast-1.7.0. Maybe it's useful for someone. make check fails (this appears to be a known problem without a solution).

pkgname=ncbi-igblast
pkgver=1.7.0
pkgrel=1
epoch=
pkgdesc="IgBLAST is a tool to analyse immunoglobulin variable domain sequences "
arch=(x86_64)
url="https://www.ncbi.nlm.nih.gov/igblast/"
license=('PUBLIC DOMAIN')
groups=()
depends=('zlib' 'bzip2' 'pcre')
makedepends=('cpio')
checkdepends=()
optdepends=()
provides=()
conflicts=()
replaces=()
backup=()
options=()
install=
changelog=
source=("ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/$pkgver/$pkgname-$pkgver-src.tar.gz")
noextract=()
md5sums=("238857cff5de770ac3fc93d96526a247")
validpgpkeys=()

prepare() {
	cd "$pkgname-$pkgver-src/c++"

	#we want to use system bzip2 und zlib anyway, see configure
	rm -r src/util/compress/bzip2
	rm -r src/util/compress/zlib
}

build() {
	cd "$pkgname-$pkgver-src/c++"
	./configure --without-internal --prefix=$pkgdir/usr --with-z=/usr/lib64/ --with-bz2=/usr/lib64/ --with-pcre=/usr/lib64/ --without-debug --without-mesa --without-opengl --without-glut --without-glew 	--without-wxwidgets --without-python --without-perl --without-boost --without-zorba --without-gbench --without-bdb 
	make -j
}

check() {
	cd "$pkgname-$pkgver-src/c++"
	
	# make -k check fails:
	#ERR [127] --  [serial/datatool] datatool.sh     (unparsable timing stats)
	#ERR [127] --  [serial/datatool] datatool_xml.sh     (unparsable timing stats)
	#this has bothered others to, see the following posts with no available solution:
	#https://lists.gnu.org/archive/html/guix-commits/2015-06/msg00720.html
}

package() {
	cd "$pkgname-$pkgver-src/c++"
	make DESTDIR="$pkgdir/" install
}