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pkgname=kraken2
pkgver=2.1.3
pkgrel=1
pkgdesc="Improved vesion of kraken ultrafast metagenomic sequence classification tool. https://doi.org/10.1186/s13059-019-1891-0"
arch=('i686' 'x86_64')
url="https://github.com/DerrickWood/kraken2"
license=('MIT')
depends=('glibc' 'gcc-libs' 'blast+' 'perl' 'bash' 'python' 'zlib')
source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DerrickWood/kraken2/archive/refs/tags/v${pkgver}.tar.gz"
'Makefile.patch'
'fastaread.patch')
sha256sums=('5269fa14adfb02e38c2da2e605e909a432d76c680d73e2e0e80e27ccd04d7c69'
'e57d358f4cc234831bf7808bb72a423ebbe13feefeba7204cd2b82fa6f3ea09b'
'40bdae9d36e7212197f32d5dc49d7d676593e0a0e0f51e7ef8c0c20ccd2d999e')
prepare() {
cp Makefile.patch ${pkgname}-${pkgver}/src
cp fastaread.patch ${pkgname}-${pkgver}/scripts
cd ${pkgname}-${pkgver}/src
# patch makefile to use $(DESTDIR) and LDFLAGS
patch -p2 < Makefile.patch
cd ../scripts
# Slighly more robust method to obtain taxid of fasta files
patch -p1 < fastaread.patch
}
build() {
cd ${pkgname}-${pkgver}/src
export KRAKEN2_DIR=/usr/lib/kraken2
make
}
package() {
cd ${pkgname}-${pkgver}/src
install -d ${pkgdir}/usr/bin
install -d ${pkgdir}/usr/lib/kraken2
install -d ${pkgdir}/usr/share/${pkgname}
make DESTDIR="${pkgdir}"/ install
cd ..
# copy kraken2 scripts to appropriate location using modified commands from 'install_kraken2.sh'
export KRAKEN2_DIR=${pkgdir}/usr/lib/kraken2
for file in scripts/*
do
perl -pl -e 'BEGIN { while (@ARGV) { $_ = shift; ($k,$v) = split /=/, $_, 2; $H{$k} = $v } }'\
-e 's/#####=(\w+)=#####/$H{$1}/g' \
"KRAKEN2_DIR=/usr/lib/kraken2" "VERSION=${pkgver}" \
< "$file" > "$KRAKEN2_DIR/$(basename $file)"
if [ -x "$file" ]
then
chmod +x "$KRAKEN2_DIR/$(basename $file)"
fi
done
cp $KRAKEN2_DIR/kraken2{,-build,-inspect} ${pkgdir}/usr/bin
install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
cp -r data/ ${pkgdir}/usr/share/${pkgname}/
}
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