Add PLINK 1.9

BioArchLinux/plink1.9/PKGBUILD

@@ -0,0 +1,38 @@
+# Maintainer: Adityarup Laha <me@adityaruplaha.me>
+pkgname='plink1.9'
+_pkgver=1.9
+pkgver=1.9.b.7.11.r64.gacb45ef4
+pkgrel=1
+pkgdesc="whole-genome association analysis toolset, version 1.9"
+arch=(x86_64)
+license=(GPL-3.0-only)
+url="https://www.cog-genomics.org/plink/1.9/"
+source=('plink1.9::git+https://github.com/chrchang/plink-ng.git'
+        'bin-name.patch')
+depends=('zlib>=1.2.4' 'cblas' 'lapack')
+makedepends=('git')
+provides=('plink1.9')
+sha256sums=(SKIP
+            24f570e751f51b6ab05c29f92cad4a57b0a54b7bb4a81dd067cf1cdc1c887327)
+
+prepare() {
+    cd "$_pkgname/$_pkgver"
+    patch -i "${srcdir}/bin-name.patch"
+}
+
+build() {
+    cd "$_pkgname/$_pkgver"
+    CFLAGS+=" -DDYNAMIC_ZLIB $(pkg-config --cflags lapack blas cblas)" CXXFLAGS+=' -DDYNAMIC_ZLIB'\
+        BLASFLAGS=$(pkg-config --libs lapack blas cblas) ZLIB=-lz \
+        LDFLAGS+=' -lpthread -lm' BIN=$_pkgname make -f Makefile
+}
+
+package() {
+    cd "$_pkgname/$_pkgver"
+    BIN="$_pkgname" DESTDIR="$pkgdir" PREFIX=/usr make -f Makefile install
+}
+
+pkgver() {
+    cd "$_pkgname"
+    echo "$_pkgver"."$(git describe --tags --long --match "v1.9*" | sed -E 's/^[^-]+-([^-]+)-([0-9]+)-(g[a-f0-9]+)/\1.r\2.\3/')"
+}

BioArchLinux/plink1.9/bin-name.patch

@@ -0,0 +1,16 @@
+diff --color -ura src/plink1.9/1.9/Makefile src/plink1.9-patched/1.9/Makefile
+--- src/plink1.9/1.9/Makefile	2024-07-26 14:43:56.962588763 +0530
++++ src/plink1.9-patched/1.9/Makefile	2024-07-26 14:45:39.865461011 +0530
+@@ -77,10 +77,10 @@
+
+ all:	$(BIN)
+
+-plink: $(OBJS)
++$(BIN): $(OBJS)
+ 	$(CXX) $(OBJS) $(LDFLAGS_EXTRA) $(BLASFLAGS) $(LDFLAGS) $(ZLIB) -o $@
+
+-plinkw: $(OBJS)
++$(BIN)w: $(OBJS)
+ 	gfortran -O2 $(OBJS) $(LDFLAGS_EXTRA) -Wl,-Bstatic $(BLASFLAGS) $(LDFLAGS) $(ZLIB) -o $@
+
+ install:

BioArchLinux/plink1.9/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: adityaruplaha
+    email: me@adityaruplaha.me
+post_build_script: |
+  git_pkgbuild_commit()
+update_on:
+  - source: github
+    github: chrchang/plink-ng
+    use_max_tag: true
+    include_regex: '^v1\.9\..*'
+    prefix: 'v'