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# Maintainer: Eric Biggers <ebiggers3 at gmail dot com>
pkgname=quake-bio # Not to be confused with Quake the game...
pkgver=0.3.1
pkgrel=2
pkgdesc="A package to correct Illumina DNA sequencing reads"
arch=("i686" "x86_64")
url="http://www.cbcb.umd.edu/software/quake"
license=("Artistic2.0")
depends=("jellyfish" "boost-libs" "r" "python2")
makedepends=("boost")
source=("http://www.cbcb.umd.edu/software/quake/downloads/quake-0.3.1.tar.gz"
"quake-${pkgver}-getopt.patch"
"quake-${pkgver}-makefile.patch"
"quake-${pkgver}-nameclash.patch"
)
build() {
cd Quake
patch -p1 < ${srcdir}/quake-${pkgver}-getopt.patch
patch -p1 < ${srcdir}/quake-${pkgver}-makefile.patch
# count-qmers and count-kmers conflict with AMOS. Just prefix all the
# binaries with `quake'.
patch -p1 < ${srcdir}/quake-${pkgver}-nameclash.patch
sed -i -e 's@jellyfish_dir\s\+=\s\+quake_dir@jellyfish_dir = "/usr/bin"@' \
bin/quake.py
sed -i -e '1s@#!/usr/bin/env python@&2@' bin/*.py
cd src
make
}
package() {
cd Quake
install -Dm644 README ${pkgdir}/usr/share/doc/quake/README
mkdir -p ${pkgdir}/usr/bin
cp bin/*.{py,r} src/quake-* ${pkgdir}/usr/bin
}
md5sums=('3f72ea0dedc8bc4c0bd0bd5c76235a93'
'ae1d6f62706b041902ec63320a40f90b'
'aa6fe2f977c9d9dd613890663c39cb2a'
'fa6529f2c0a0eb7a7f165a44691df5b2')
md5sums=('3f72ea0dedc8bc4c0bd0bd5c76235a93'
'ae1d6f62706b041902ec63320a40f90b'
'aa6fe2f977c9d9dd613890663c39cb2a'
'57b3720c486ba71bd9dcd8e730134cfd')
md5sums=('3f72ea0dedc8bc4c0bd0bd5c76235a93'
'ae1d6f62706b041902ec63320a40f90b'
'aa6fe2f977c9d9dd613890663c39cb2a'
'c4acdbddf1d4e01c813ced61aec9d135')
|