From ff3df74782736c3e3eaa87556776211a761795dd Mon Sep 17 00:00:00 2001
From: starsareintherose <starsareintherose@outlook.com>
Date: Thu, 26 Aug 2021 23:45:46 +0800
Subject: [PATCH] add raxml

---
 raxml/PKGBUILD      | 41 +++++++++++++++++++++++++++++++++++++++++
 raxml/lilac.py      | 10 ++++++++++
 raxml/lilac.yaml    |  8 ++++++++
 raxml/raxml.install | 17 +++++++++++++++++
 4 files changed, 76 insertions(+)
 create mode 100644 raxml/PKGBUILD
 create mode 100644 raxml/lilac.py
 create mode 100644 raxml/lilac.yaml
 create mode 100644 raxml/raxml.install

diff --git a/raxml/PKGBUILD b/raxml/PKGBUILD
new file mode 100644
index 0000000000..43ffc1ccf6
--- /dev/null
+++ b/raxml/PKGBUILD
@@ -0,0 +1,41 @@
+# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
+
+pkgname=raxml
+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=('bash' 'perl')
+conflicts=(raxml-mpi)
+install='raxml.install'
+source=("$pkgname-$pkgver.tar.gz::https://github.com/stamatak/standard-RAxML/archive/v$pkgver.tar.gz"
+        'raxml.install')
+sha256sums=('338f81b52b54e16090e193daf36c1d4baa9b902705cfdc7f4497e3e09718533b'
+            'c908ecbcfd6323e0b05a19037f96904a9b379ae0a9934ade839210095bb49caf')
+
+build() {
+  cd standard-RAxML-$pkgver
+
+  for _f in $(ls Makefile*gcc | grep -vE "HYBRID|MPI") ; 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/lilac.py b/raxml/lilac.py
new file mode 100644
index 0000000000..8c66f58ed6
--- /dev/null
+++ b/raxml/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/lilac.yaml b/raxml/lilac.yaml
new file mode 100644
index 0000000000..dffeb0346a
--- /dev/null
+++ b/raxml/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/raxml.install b/raxml/raxml.install
new file mode 100644
index 0000000000..bbc5aac06e
--- /dev/null
+++ b/raxml/raxml.install
@@ -0,0 +1,17 @@
+post_install() {
+cat << EOF
+
+raxml has installed all buildable executables, which ones depends on
+your hardware (AVX, AVX2, SSE)
+
+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
+}