From 1bf5c81f76fb707b58031e28cf055024946deb47 Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Sat, 23 Apr 2022 00:30:19 +0100
Subject: [PATCH] add two beagle version

---
 BioArchLinux/mrbayes-beagle/PKGBUILD       | 32 ++++++++++++++++++++
 BioArchLinux/mrbayes-beagle/lilac.py       | 10 +++++++
 BioArchLinux/mrbayes-beagle/lilac.yaml     | 10 +++++++
 BioArchLinux/mrbayes-mpi-beagle/PKGBUILD   | 35 ++++++++++++++++++++++
 BioArchLinux/mrbayes-mpi-beagle/lilac.py   | 11 +++++++
 BioArchLinux/mrbayes-mpi-beagle/lilac.yaml | 10 +++++++
 6 files changed, 108 insertions(+)
 create mode 100644 BioArchLinux/mrbayes-beagle/PKGBUILD
 create mode 100644 BioArchLinux/mrbayes-beagle/lilac.py
 create mode 100644 BioArchLinux/mrbayes-beagle/lilac.yaml
 create mode 100644 BioArchLinux/mrbayes-mpi-beagle/PKGBUILD
 create mode 100644 BioArchLinux/mrbayes-mpi-beagle/lilac.py
 create mode 100644 BioArchLinux/mrbayes-mpi-beagle/lilac.yaml

diff --git a/BioArchLinux/mrbayes-beagle/PKGBUILD b/BioArchLinux/mrbayes-beagle/PKGBUILD
new file mode 100644
index 0000000000..af427ef712
--- /dev/null
+++ b/BioArchLinux/mrbayes-beagle/PKGBUILD
@@ -0,0 +1,32 @@
+# Original: Abhishek Dasgupta <abhidg@gmail.com>
+# Maintainer: Stunts <f.pinamartins@gmail.com>
+pkgname=mrbayes-beagle
+_up_pkgname=MrBayes
+pkgver=3.2.7
+pkgrel=5
+provides=("mrbayes")
+pkgdesc="A program for the Bayesian estimation of phylogeny. https://doi.org/10.1093/sysbio/sys029"
+arch=('i686' 'x86_64')
+license=('GPL')
+url="http://nbisweden.github.io/MrBayes/"
+depends=('readline' 'gcc' 'beagle-lib')
+source=(https://github.com/NBISweden/MrBayes/archive/v${pkgver}.tar.gz)
+sha256sums=('64da39c01f606d0413ce90a1dd3c1ce2cbdef4cbad99aee8a4b2391a2e8db244')
+
+build() {
+  cd ${srcdir}/${_up_pkgname}-${pkgver}
+  #Build with beagle-lib support if available:
+  if [ -f /usr/lib/libhmsbeagle.so ]
+  then
+    msg "beagle-lib found! Building with CUDA support."
+    ./configure --with-beagle=/usr --prefix=${pkgdir}/usr
+  else
+    msg "beagle-lib not found! Building without CUDA support."
+    ./configure --with-beagle=no --prefix=${pkgdir}/usr
+  fi
+  make
+}
+package() {
+  cd ${srcdir}/${_up_pkgname}-${pkgver}
+  make install
+}
diff --git a/BioArchLinux/mrbayes-beagle/lilac.py b/BioArchLinux/mrbayes-beagle/lilac.py
new file mode 100644
index 0000000000..8c66f58ed6
--- /dev/null
+++ b/BioArchLinux/mrbayes-beagle/lilac.py
@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
diff --git a/BioArchLinux/mrbayes-beagle/lilac.yaml b/BioArchLinux/mrbayes-beagle/lilac.yaml
new file mode 100644
index 0000000000..4c43e762cf
--- /dev/null
+++ b/BioArchLinux/mrbayes-beagle/lilac.yaml
@@ -0,0 +1,10 @@
+build_prefix: multilib
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: github
+    github: NBISweden/MrBayes
+    use_latest_release: true
+repo_depends:
+  - beagle-lib
diff --git a/BioArchLinux/mrbayes-mpi-beagle/PKGBUILD b/BioArchLinux/mrbayes-mpi-beagle/PKGBUILD
new file mode 100644
index 0000000000..22bb51f278
--- /dev/null
+++ b/BioArchLinux/mrbayes-mpi-beagle/PKGBUILD
@@ -0,0 +1,35 @@
+# Maintainer: Guoyi ("malacology") <guoyizhang at malacology.net>
+# Contributor: Guoyi ("malacology") <guoyizhang at malacology.net>
+# Contributor: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
+
+pkgname=mrbayes-mpi-beagle
+pkgver=3.2.7
+pkgrel=6
+pkgdesc="MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. https://doi.org/10.1093/sysbio/sys029"
+arch=('i686' 'x86_64')
+url="nbisweden.github.io/mrbayes/"
+license=('GPL3')
+depends=('openmpi' 'readline' 'gcc' 'beagle-lib')
+conflicts=(mrbayes)
+provides=(mrbayes)
+source=("https://github.com/NBISweden/MrBayes/archive/v${pkgver}.tar.gz")
+sha256sums=('64da39c01f606d0413ce90a1dd3c1ce2cbdef4cbad99aee8a4b2391a2e8db244')
+
+build() {
+  cd ${srcdir}/MrBayes-$pkgver
+  #Build with beagle-lib support if available:
+  if [ -f /usr/lib/libhmsbeagle.so ]
+  then
+    msg "beagle-lib found! Building with CUDA support."
+    ./configure --with-beagle=/usr --prefix=${pkgdir}/usr --enable-mpi=yes
+  else
+    msg "beagle-lib not found! Building without CUDA support."
+    ./configure --with-beagle=no --prefix=${pkgdir}/usr --enable-mpi=yes
+  fi
+  make
+}
+package() {
+  cd ${srcdir}/MrBayes-$pkgver
+  make install
+  install ${pkgdir}/usr/bin/mb ${pkgdir}/usr/bin/mb-mpi
+}
diff --git a/BioArchLinux/mrbayes-mpi-beagle/lilac.py b/BioArchLinux/mrbayes-mpi-beagle/lilac.py
new file mode 100644
index 0000000000..14e434f168
--- /dev/null
+++ b/BioArchLinux/mrbayes-mpi-beagle/lilac.py
@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+  update_aur_repo()
diff --git a/BioArchLinux/mrbayes-mpi-beagle/lilac.yaml b/BioArchLinux/mrbayes-mpi-beagle/lilac.yaml
new file mode 100644
index 0000000000..4c43e762cf
--- /dev/null
+++ b/BioArchLinux/mrbayes-mpi-beagle/lilac.yaml
@@ -0,0 +1,10 @@
+build_prefix: multilib
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: github
+    github: NBISweden/MrBayes
+    use_latest_release: true
+repo_depends:
+  - beagle-lib