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-rw-r--r--.SRCINFO11
-rw-r--r--.gitignore3
-rw-r--r--PKGBUILD45
3 files changed, 27 insertions, 32 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 11e4f913ab1f..38bb8418cee3 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -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
diff --git a/PKGBUILD b/PKGBUILD
index 6bd188beb418..83af8c6365c5 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -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')