From b94030cc5ddf74c664d4a9fdf7b0f45f85c675e6 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Tue, 10 Jan 2023 18:55:45 -0600
Subject: plink: add new version (#34741)

The distribution of this has jumped around a bit. I left the previous
versions as-is.
---
 .../builtin/packages/plink/dynamic_zlib.patch      | 70 ++++++++++++++++++++++
 var/spack/repos/builtin/packages/plink/package.py  | 30 ++++++++--
 2 files changed, 96 insertions(+), 4 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/plink/dynamic_zlib.patch

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/plink/dynamic_zlib.patch b/var/spack/repos/builtin/packages/plink/dynamic_zlib.patch
new file mode 100644
index 0000000000..301f4a0eda
--- /dev/null
+++ b/var/spack/repos/builtin/packages/plink/dynamic_zlib.patch
@@ -0,0 +1,70 @@
+diff -ur a/1.9/dose2plink.c b/1.9/dose2plink.c
+--- a/1.9/dose2plink.c	2022-12-19 11:00:05.000000000 -0600
++++ b/1.9/dose2plink.c	2022-12-19 13:08:50.022275377 -0600
+@@ -15,6 +15,8 @@
+ // You should have received a copy of the GNU General Public License
+ // along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ 
++#include "plink_common.h"
++
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
+@@ -96,7 +98,11 @@
+   #endif
+ #endif
+ 
+-#include "../zlib-1.2.12/zlib.h"
++#ifdef DYNAMIC_ZLIB
++  #include <zlib.h>
++#else
++  #include "../zlib-1.2.12/zlib.h"
++#endif
+ 
+ #ifdef __APPLE__
+   #include <sys/sysctl.h>
+diff -ur a/1.9/pigz.c b/1.9/pigz.c
+--- a/1.9/pigz.c	2022-12-19 11:00:05.000000000 -0600
++++ b/1.9/pigz.c	2022-12-19 13:06:08.562023953 -0600
+@@ -485,6 +485,8 @@
+ }
+ #else
+ 
++#include "pigz.h"
++
+ #define VERSION "pigz 2.3\n"
+ 
+ /* use large file functions if available */
+@@ -543,8 +545,6 @@
+                            release(), peek_lock(), free_lock(), yarn_name */
+ #endif
+ 
+-#include "pigz.h"
+-
+ 
+ /* for local functions and globals */
+ #define local static
+diff -ur a/1.9/pigz.h b/1.9/pigz.h
+--- a/1.9/pigz.h	2022-12-19 11:00:05.000000000 -0600
++++ b/1.9/pigz.h	2022-12-19 12:58:40.385103423 -0600
+@@ -1,6 +1,8 @@
+ #ifndef __PIGZ_H__
+ #define __PIGZ_H__
+ 
++#include "plink_common.h"
++
+ #include <stdint.h>
+ #include <inttypes.h>
+ 
+diff -ur a/1.9/plink_common.h b/1.9/plink_common.h
+--- a/1.9/plink_common.h	2022-12-19 11:00:06.000000000 -0600
++++ b/1.9/plink_common.h	2022-12-19 12:58:06.819259147 -0600
+@@ -41,6 +41,8 @@
+ // Uncomment this to build this without CBLAS/CLAPACK.
+ // #define NOLAPACK
+ 
++#define DYNAMIC_ZLIB
++
+ // Uncomment this to prevent all unstable features from being accessible from
+ // the command line.
+ #define STABLE_BUILD
diff --git a/var/spack/repos/builtin/packages/plink/package.py b/var/spack/repos/builtin/packages/plink/package.py
index b1e549052e..21ba61a82b 100644
--- a/var/spack/repos/builtin/packages/plink/package.py
+++ b/var/spack/repos/builtin/packages/plink/package.py
@@ -13,6 +13,11 @@ class Plink(Package):
 
     homepage = "https://www.cog-genomics.org/plink/1.9/"
 
+    version(
+        "1.9-beta6.27",
+        commit="a2ea957c893fbb0558358edef27f3ecbf3d360f8",
+        git="https://github.com/chrchang/plink-ng.git",
+    )
     version(
         "1.9-beta6.10",
         sha256="f8438656996c55a5edd95c223cce96277de6efaab1b9b1d457bfee0c272058d8",
@@ -30,10 +35,15 @@ class Plink(Package):
         preferred=True,
     )
 
-    depends_on("atlas", when="@1.9-beta5")
-    depends_on("netlib-lapack", when="@1.9-beta5")
-    depends_on("atlas", when="@1.9-beta6.10")
-    depends_on("netlib-lapack", when="@1.9-beta6.10")
+    depends_on("atlas", when="@1.9-beta5:1.9-beta6.10")
+    depends_on("netlib-lapack", when="@1.9-beta5:1.9-beta6.10")
+
+    with when("@1.9-beta-6.27:"):
+        depends_on("zlib", when="@1.9-beta6.27:")
+        depends_on("blas", when="@1.9-beta6.27:")
+        depends_on("lapack", when="@1.9-beta6.27:")
+
+    patch("dynamic_zlib.patch", when="@1.9-beta6.27:")
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
@@ -47,3 +57,15 @@ class Plink(Package):
                 install("plink", prefix.bin)
         if spec.version == Version("1.9-beta6.10"):
             install("plink", prefix.bin)
+
+    @when("@1.9-beta6.27:")
+    def setup_build_environment(self, env):
+        env.set("BLASFLAGS", self.spec["blas"].libs.ld_flags)
+        env.set("ZLIB", self.spec["zlib"].libs.ld_flags)
+
+    @when("@1.9-beta6.27:")
+    def install(self, spec, prefix):
+        with working_dir("1.9"):
+            make()
+            mkdir(prefix.bin)
+            install("plink", prefix.bin)
-- 
cgit v1.2.3-70-g09d2