From 2bafa4a4d49e7e238dc728925b3977260a4508a2 Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Thu, 6 Feb 2025 17:30:16 +1100
Subject: [PATCH] muscle3: add for ipyrad

---
 BioArchLinux/muscle3/PKGBUILD   | 30 ++++++++++++++++++++++++++++++
 BioArchLinux/muscle3/lilac.yaml |  8 ++++++++
 2 files changed, 38 insertions(+)
 create mode 100644 BioArchLinux/muscle3/PKGBUILD
 create mode 100644 BioArchLinux/muscle3/lilac.yaml

diff --git a/BioArchLinux/muscle3/PKGBUILD b/BioArchLinux/muscle3/PKGBUILD
new file mode 100644
index 0000000000..d0f4e9b0d1
--- /dev/null
+++ b/BioArchLinux/muscle3/PKGBUILD
@@ -0,0 +1,30 @@
+# Maintainer: Michael Schubert <mschu.dev at gmail>
+# Contributor: Mick Elliot <micke@sfu.ca>
+# Contributor: Damir Perisa <damir.perisa@bluewin.ch>
+pkgname=muscle3
+pkgver=3.8.1551
+pkgrel=2
+pkgdesc="multiple sequence comparison by log-expectation"
+arch=('i686' 'x86_64')
+url="http://www.drive5.com/muscle/"
+license=('custom')
+source=(http://www.drive5.com/muscle/muscle_src_$pkgver.tar.gz LICENSE)
+sha256sums=('c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'
+            '2ee887dede5d3ddb6fa65690e0afd8d1083d835522d9271450752df0cc2f6658')
+provides=('muscle')
+conflicts=('muscle')
+build() {
+  cd "$srcdir"
+  if [ "${CARCH}" = "i686" ]; then
+    make CFLAGS=" -march=i686 -mtune=generic -O2 -pipe" LDLIBS=" -lm"
+  else
+    make CFLAGS=" -march=x86-64 -mtune=generic -O2 -pipe" LDLIBS=" -lm"
+  fi
+}
+
+package() {
+  cd "$srcdir"
+  install -D -m755 muscle "$pkgdir/usr/bin/muscle"
+  install -D -m644 "$srcdir/LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}
+ 
diff --git a/BioArchLinux/muscle3/lilac.yaml b/BioArchLinux/muscle3/lilac.yaml
new file mode 100644
index 0000000000..0b3467a632
--- /dev/null
+++ b/BioArchLinux/muscle3/lilac.yaml
@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: muscle_src_(\d+.\d+.\d+).tar.gz
+    source: regex
+    url: http://www.drive5.com/muscle/downloads.htm