iqtree: enable LSD2 library

BioArchLinux/iqtree/PKGBUILD

@@ -1,34 +1,32 @@
-# Maintainer: Dominik Schrempf <dominik dot schrempf at gmail dot com>
+# Maintainer: Guoyi Zhang <myname at malacology dot net>
-
-# 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
 
 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')
+depends=('boost' 'eigen' 'gcc-libs' 'zlib')
-makedepends=('cmake' 'make' 'gcc')
+makedepends=('cmake' 'make' 'gcc' 'git')
-source=("iqtree2-$pkgver::https://github.com/iqtree/iqtree2/archive/v${pkgver}.tar.gz")
+source=("git+$url.git#tag=v${pkgver}")
-md5sums=('83e85d78b096b48607b7dbf91f8211a9')
+md5sums=('SKIP')
+
+prepare() {
+  cd $_pkgname
+  git submodule update --init --recursive
+}
 
 build() {
-  cd iqtree2-${pkgver}
+  cd $_pkgname
-  mkdir -p build
+  mkdir -p build && cd build
-  cd build
   cmake -DIQTREE_FLAGS=omp ..
-  make || bash -c "df -h"
+  make
 }
 
 package() {
-  mkdir -p ${pkgdir}/usr/bin
+  cd $_pkgname/build 
-  cd "$srcdir"/iqtree2-${pkgver}/build 
+  chmod +x $_pkgname
-  chmod +x iqtree2
+  install -Dm 755 $_pkgname ${pkgdir}/usr/bin/$pkgname
-  mv iqtree2 ${pkgdir}/usr/bin/iqtree
 }