From e6d11224a4e5f1d815e39a58ce20417ec924d0f5 Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Mon, 29 Aug 2022 16:47:15 +0100
Subject: [PATCH] generax: init

---
 BioArchLinux/generax/PKGBUILD      | 36 ++++++++++++++++++++++++++++++
 BioArchLinux/generax/generax.patch | 12 ++++++++++
 BioArchLinux/generax/lilac.py      | 12 ++++++++++
 BioArchLinux/generax/lilac.yaml    |  9 ++++++++
 4 files changed, 69 insertions(+)
 create mode 100644 BioArchLinux/generax/PKGBUILD
 create mode 100644 BioArchLinux/generax/generax.patch
 create mode 100644 BioArchLinux/generax/lilac.py
 create mode 100644 BioArchLinux/generax/lilac.yaml

diff --git a/BioArchLinux/generax/PKGBUILD b/BioArchLinux/generax/PKGBUILD
new file mode 100644
index 0000000000..dead770e04
--- /dev/null
+++ b/BioArchLinux/generax/PKGBUILD
@@ -0,0 +1,36 @@
+pkgname=generax
+_pkgname=GeneRax
+pkgver=2.0.4
+pkgrel=1
+arch=('x86_64')
+url="https://github.com/BenoitMorel/GeneRax"
+pkgdescr="A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene  Family Tree Inference under Gene Duplication, Transfer, and Loss https://doi.org/10.1093/molbev/msaa141"
+depends=('gcc-libs' 'gmp')
+makedepends=('cmake' 'make' 'gcc' 'openmpi'  'bison' 'flex' 'git')
+license=('AGPL')
+source=("git+$url.git#tag=$pkgver"
+		"$pkgname.patch")
+md5sums=('SKIP'
+         'e11bd9f6fbedfb6e47b5b4a29dde98a0')
+
+prepare(){
+  cd $_pkgname
+  git submodule update --init --recursive
+  patch -p1 -i "${srcdir}/$pkgname.patch" #for 2.0.4
+}
+
+build() {
+  cd $_pkgname
+  mkdir -p build && cd build
+  cmake ..
+  make
+}
+
+package() {
+  cd $_pkgname
+  cd build/bin
+for bin in $(ls)
+do
+	install -Dm 755 $bin $pkgdir/usr/bin/$bin
+done
+}
diff --git a/BioArchLinux/generax/generax.patch b/BioArchLinux/generax/generax.patch
new file mode 100644
index 0000000000..20728f8540
--- /dev/null
+++ b/BioArchLinux/generax/generax.patch
@@ -0,0 +1,12 @@
+diff --git a/src/core/IO/Model.hpp b/src/core/IO/Model.hpp
+index 0eb6ce1..3a16942 100644
+--- a/src/core/IO/Model.hpp
++++ b/src/core/IO/Model.hpp
+@@ -6,6 +6,7 @@
+ 
+ #include <algorithm>
+ #include <unordered_map>
++#include <stdexcept>
+ extern "C" {
+ #include <pll.h>
+ #include <pllmod_algorithm.h>
diff --git a/BioArchLinux/generax/lilac.py b/BioArchLinux/generax/lilac.py
new file mode 100644
index 0000000000..c6d1de3db7
--- /dev/null
+++ b/BioArchLinux/generax/lilac.py
@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+  update_aur_repo()
diff --git a/BioArchLinux/generax/lilac.yaml b/BioArchLinux/generax/lilac.yaml
new file mode 100644
index 0000000000..88a0e43bf5
--- /dev/null
+++ b/BioArchLinux/generax/lilac.yaml
@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - source: github
+    github: BenoitMorel/GeneRax
+    use_latest_release: true
+    prefix: 'v'