diff options
-rw-r--r-- | .SRCINFO | 11 | ||||
-rw-r--r-- | .gitignore | 3 | ||||
-rw-r--r-- | PKGBUILD | 45 |
3 files changed, 27 insertions, 32 deletions
@@ -1,17 +1,14 @@ pkgbase = samtools pkgdesc = tools for manipulating next-generation sequencing data - pkgver = 1.8 + pkgver = 1.19.2 pkgrel = 1 url = http://www.htslib.org/ arch = i686 arch = x86_64 license = custom - depends = htslib + depends = htslib>=1.19.1 optdepends = luajit: needed for r2plot.lua vcfutils.lua - optdepends = python2: needed for varfilter.py - options = staticlibs - source = https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2 - md5sums = c6e981c92ca00a44656a708c4b52aba3 + source = samtools-1.19.2.tar.bz2::https://github.com/samtools/samtools/releases/download/1.19.2/samtools-1.19.2.tar.bz2 + sha256sums = 71f60499668e4c08e7d745fbff24c15cc8a0977abab1acd5d2bb419bdb065e96 pkgname = samtools - diff --git a/.gitignore b/.gitignore index 42ab3cf03f2d..ab3333456c2a 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,4 @@ *.pkg.tar* +*.tar.bz2 +pkg +src @@ -1,32 +1,30 @@ -# Maintainer: Alex Peltzer ("alexpe87") <alexpe.aur@mailbox.org> +# Maintainer: r6eve <r6eve at acm dot org> +# Former Maintainer (thanks!) : Christopher Vittal ("viralstitch") <chris@vittal.dev> +# Former Maintainer (thanks!) : Alex Peltzer ("alexpe87") <alexpe.aur@mailbox.org> # Former Maintainer (thanks dude!) : Christian Krause ("wookietreiber") <christian.krause@mailbox.org> # Contributor: Markus Heuser <markus.heuser@web.de> pkgname=samtools -pkgver=1.8 +pkgver=1.19.2 pkgrel=1 pkgdesc="tools for manipulating next-generation sequencing data" arch=('i686' 'x86_64') url="http://www.htslib.org/" license=('custom') -depends=('htslib') -optdepends=('luajit: needed for r2plot.lua vcfutils.lua' - 'python2: needed for varfilter.py') -options=('staticlibs') -source=(https://github.com/samtools/samtools/releases/download/$pkgver/$pkgname-$pkgver.tar.bz2) +depends=('htslib>=1.19.1') +optdepends=('luajit: needed for r2plot.lua vcfutils.lua') +source=("${pkgname}-${pkgver}.tar.bz2"::"https://github.com/samtools/samtools/releases/download/${pkgver}/${pkgname}-${pkgver}.tar.bz2") +sha256sums=('71f60499668e4c08e7d745fbff24c15cc8a0977abab1acd5d2bb419bdb065e96') prepare() { - cd $srcdir/$pkgname-$pkgver + cd "${srcdir}/${pkgname}-${pkgver}" # prevent shipped htslib to be used - rm -rf htslib-$pkgver || exit 1 - - sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \ - -i misc/varfilter.py + rm -rf "htslib-${pkgver}" || exit 1 } build() { - cd $srcdir/$pkgname-$pkgver + cd "${srcdir}/${pkgname}-${pkgver}" ./configure \ --prefix=/usr \ @@ -36,26 +34,23 @@ build() { } check() { - cd $srcdir/$pkgname-$pkgver + cd "${srcdir}/${pkgname}-${pkgver}" make check } package() { - cd $srcdir/$pkgname-$pkgver + cd ${srcdir}/${pkgname}-${pkgver} - make DESTDIR=$pkgdir install + make DESTDIR=${pkgdir} install - for file in misc/*.lua ; do - install -Dm755 $file $pkgdir/usr/bin/$(basename $file) + # Install non-Perl misc/ programs + for file in misc/*.lua; do + install -Dm755 "${file}" "${pkgdir}/usr/bin/$(basename "${file}")" done - install -d $pkgdir/usr/include/bam - install -Dm644 *.h $pkgdir/usr/include/bam - - install -Dm644 libbam.a $pkgdir/usr/lib/libbam.a + install -d "${pkgdir}/usr/include/bam" + install -Dm644 *.h "${pkgdir}/usr/include/bam" - install -Dm644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE + install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE" } - -md5sums=('c6e981c92ca00a44656a708c4b52aba3') |