Initial upload: bwa-mem2 2.2.1-1

Add bwa-mem2

3 files changed, 74 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..a3482dc81096
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,14 @@
+pkgbase = bwa-mem2
+	pkgdesc = The next version of Burrows-Wheeler Aligner MEM algorithm
+	pkgver = 2.2.1
+	pkgrel = 1
+	url = https://github.com/bwa-mem2/bwa-mem2
+	arch = x86_64
+	license = MIT
+	depends = zlib
+	source = bwa-mem2-2.2.1.tar.gz::https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/Source_code_including_submodules.tar.gz
+	source = gcc_rdtsc.patch
+	sha256sums = 9b001bdc7666ee3f14f3698b21673714d429af50438b894313b05bc4688b1f6d
+	sha256sums = 50556ad538edb98bbdcaae4338dc42873e6aae27ab7ab4a090cd0442818072f9
+
+pkgname = bwa-mem2
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..c01d7004fc29
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,47 @@
+# Maintainer: Charles Vejnar <first name [dot] last name [at] gmail [dot] com>
+# Contributor: Maël Kerbiriou <m431.kerbiriou@gmail.com>
+
+pkgname=bwa-mem2
+pkgver=2.2.1
+pkgrel=1
+pkgdesc="The next version of Burrows-Wheeler Aligner MEM algorithm"
+arch=("x86_64")
+url="https://github.com/bwa-mem2/bwa-mem2"
+license=("MIT")
+depends=('zlib')
+source=("$pkgname-$pkgver.tar.gz::https://github.com/bwa-mem2/bwa-mem2/releases/download/v${pkgver}/Source_code_including_submodules.tar.gz"
+        "gcc_rdtsc.patch")
+sha256sums=('9b001bdc7666ee3f14f3698b21673714d429af50438b894313b05bc4688b1f6d'
+            '50556ad538edb98bbdcaae4338dc42873e6aae27ab7ab4a090cd0442818072f9')
+
+# For compiling for native instruction set only, set this to false:
+MULTI=${MULTI:-true}
+
+prepare() {
+    cd "$srcdir/$pkgname-${pkgver}"
+
+    patch -p1 -i "${srcdir}/gcc_rdtsc.patch"
+}
+
+build() {
+    cd "$srcdir/$pkgname-${pkgver}"
+
+    if [ "$MULTI" = true ] ; then
+        make multi
+    else
+        make arch=native
+    fi
+}
+
+package() {
+    cd "$srcdir/$pkgname-${pkgver}"
+
+    install -Dm755 bwa-mem2 "$pkgdir/usr/bin/bwa-mem2"
+    install -Dm644 LICENSE "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+
+    if [ "$MULTI" = true ] ; then
+        install -Dm755 bwa-mem2.avx2      "$pkgdir/usr/bin/bwa-mem2.avx2"
+        install -Dm755 bwa-mem2.avx512bw  "$pkgdir/usr/bin/bwa-mem2.avx512bw"
+        install -Dm755 bwa-mem2.sse41     "$pkgdir/usr/bin/bwa-mem2.sse41"
+    fi
+}
diff --git a/gcc_rdtsc.patch b/gcc_rdtsc.patch
new file mode 100644
index 000000000000..411da804d008
--- /dev/null
+++ b/gcc_rdtsc.patch
@@ -0,0 +1,13 @@
+diff --git a/src/utils.h b/src/utils.h
+index 54a062a..e3037a3 100644
+--- a/src/utils.h
++++ b/src/utils.h
+@@ -48,7 +48,7 @@
+ 
+ #define xassert(cond, msg) if ((cond) == 0) _err_fatal_simple_core(__func__, msg)
+ 
+-#if defined(__GNUC__) && !defined(__clang__)
++#if defined(__GNUC__) &&  __GNUC__ < 11 && !defined(__clang__)
+ #if defined(__i386__)
+ static inline unsigned long long __rdtsc(void)
+ {