From d4549fb306d6524719730073f142ccae7da7534b Mon Sep 17 00:00:00 2001
From: starsareintherose <starsareintherose@outlook.com>
Date: Thu, 26 Aug 2021 23:46:04 +0800
Subject: [PATCH] add raxml-mpi

---
 raxml-mpi/PKGBUILD      | 43 +++++++++++++++++++++++++++++++++++++++++
 raxml-mpi/lilac.py      | 10 ++++++++++
 raxml-mpi/lilac.yaml    |  8 ++++++++
 raxml-mpi/raxml.install | 21 ++++++++++++++++++++
 4 files changed, 82 insertions(+)
 create mode 100644 raxml-mpi/PKGBUILD
 create mode 100644 raxml-mpi/lilac.py
 create mode 100644 raxml-mpi/lilac.yaml
 create mode 100644 raxml-mpi/raxml.install

diff --git a/raxml-mpi/PKGBUILD b/raxml-mpi/PKGBUILD
new file mode 100644
index 0000000000..72f2bad801
--- /dev/null
+++ b/raxml-mpi/PKGBUILD
@@ -0,0 +1,43 @@
+# Contributor: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
+# Maintainer: Stefan Husmann <stefan-husmann@t-online.de>
+
+pkgname=raxml-mpi
+pkgver=8.2.12
+pkgrel=1
+pkgdesc="Randomized Axelerated Maximum Likelihood"
+arch=('x86_64')
+url="http://sco.h-its.org/exelixis/web/software/raxml/"
+license=('GPL3')
+depends=('openmpi')
+conflicts=(raxml)
+provides=(raxml)
+install='raxml.install'
+source=("raxml-$pkgver.tar.gz::https://github.com/stamatak/standard-RAxML/archive/v$pkgver.tar.gz"
+        'raxml.install')
+sha256sums=('338f81b52b54e16090e193daf36c1d4baa9b902705cfdc7f4497e3e09718533b'
+            '05283dec7f44c560590555b4f901e0c1ed422892471bddf651d90c94b41716ea')
+
+build() {
+  cd standard-RAxML-$pkgver
+
+  for _f in Makefile*gcc ; do
+    rm -f *.o
+    make -f $_f || true
+  done
+}
+
+package() {
+  cd standard-RAxML-$pkgver
+
+  for _f in raxml* ; do
+    install -Dm755 $_f "$pkgdir"/usr/bin/$(basename $_f)
+  done
+
+  for _perlscript in usefulScripts/*.pl ; do
+    install -Dm755 $_perlscript "$pkgdir"/usr/bin/$(basename $_perlscript .pl)
+  done
+
+  for _shellscript in usefulScripts/*.sh ; do
+    install -Dm755 $_shellscript "$pkgdir"/usr/bin/$(basename $_shellscript .sh)
+  done
+}
diff --git a/raxml-mpi/lilac.py b/raxml-mpi/lilac.py
new file mode 100644
index 0000000000..8c66f58ed6
--- /dev/null
+++ b/raxml-mpi/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/raxml-mpi/lilac.yaml b/raxml-mpi/lilac.yaml
new file mode 100644
index 0000000000..dffeb0346a
--- /dev/null
+++ b/raxml-mpi/lilac.yaml
@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: github
+    github: stamatak/standard-RAxML
+    use_latest_release: true
diff --git a/raxml-mpi/raxml.install b/raxml-mpi/raxml.install
new file mode 100644
index 0000000000..abacf68491
--- /dev/null
+++ b/raxml-mpi/raxml.install
@@ -0,0 +1,21 @@
+post_install() {
+cat << EOF
+
+raxml has installed all buildable executables, falling into categories
+
+1.  your hardware (AVX, AVX2, SSE)
+2.  parallel pthreads versions
+3.  coarse grained MPI versions
+4.  hybrid MPI/pthreads versions
+
+if you either want (or need) an executable that is just called raxml,
+create a symlink like this to your preferred variant:
+
+    ln -s /usr/bin/raxmlHPC-PTHREADS-AVX2 /usr/bin/raxml
+
+EOF
+}
+
+post_upgrade() {
+  post_install
+}