From a8231e64b4ee9b2cde4f98cd8602c2a855076ad6 Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Mon, 29 Aug 2022 19:48:54 +0100
Subject: [PATCH] iqtree: enable LSD2 library

---
 BioArchLinux/iqtree/PKGBUILD | 38 +++++++++++++++++-------------------
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/BioArchLinux/iqtree/PKGBUILD b/BioArchLinux/iqtree/PKGBUILD
index f5c5c00a6d..cfe0a49366 100644
--- a/BioArchLinux/iqtree/PKGBUILD
+++ b/BioArchLinux/iqtree/PKGBUILD
@@ -1,34 +1,32 @@
-# Maintainer: Dominik Schrempf <dominik dot schrempf at gmail dot com>
-
-# XXX: The following warning cannot be removed because CMAKE stores the build
-# directory in the executable 'iqtree'.
-
-# ==> WARNING: Package contains reference to $srcdir
-# usr/bin/iqtree
+# Maintainer: Guoyi Zhang <myname at malacology dot net>
 
 pkgname=iqtree
+_pkgname=iqtree2
 pkgver=2.1.2
 pkgrel=2
 pkgdesc="Efficient phylogenomic software by maximum likelihood; multicore version (OMP). https://doi.org/10.1093/molbev/msaa015"
 arch=(x86_64)
-url="http://www.iqtree.org/"
+url="https://github.com/iqtree/iqtree2"
 license=('GPL2')
-depends=('boost' 'eigen' 'glibc' 'zlib')
-makedepends=('cmake' 'make' 'gcc')
-source=("iqtree2-$pkgver::https://github.com/iqtree/iqtree2/archive/v${pkgver}.tar.gz")
-md5sums=('83e85d78b096b48607b7dbf91f8211a9')
+depends=('boost' 'eigen' 'gcc-libs' 'zlib')
+makedepends=('cmake' 'make' 'gcc' 'git')
+source=("git+$url.git#tag=v${pkgver}")
+md5sums=('SKIP')
+
+prepare() {
+  cd $_pkgname
+  git submodule update --init --recursive
+}
 
 build() {
-  cd iqtree2-${pkgver}
-  mkdir -p build
-  cd build
+  cd $_pkgname
+  mkdir -p build && cd build
   cmake -DIQTREE_FLAGS=omp ..
-  make || bash -c "df -h"
+  make
 }
 
 package() {
-  mkdir -p ${pkgdir}/usr/bin
-  cd "$srcdir"/iqtree2-${pkgver}/build 
-  chmod +x iqtree2
-  mv iqtree2 ${pkgdir}/usr/bin/iqtree
+  cd $_pkgname/build 
+  chmod +x $_pkgname
+  install -Dm 755 $_pkgname ${pkgdir}/usr/bin/$pkgname
 }