plink2 installs with patched Makefile

gn/packages/bioinformatics.scm

@@ -22,6 +22,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages cpio)
   #:use-module (gnu packages file)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
@@ -173,30 +174,27 @@ confidence region for the location of a putative QTL.")
        (patches (list (search-patch "plink-ng-Makefile-zlib.patch")))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #t ;no "check" target
-       #:make-flags (list (string-append "LIB_LAPACK="
-                                         (assoc-ref %build-inputs "lapack")
-                                         "/lib/liblapack.so")
-                          "WITH_LAPACK=1"
-                          "FORCE_DYNAMIC=1"
-                          ;; disable phoning home
-                          "WITH_WEBCHECK=")
+     '(#:tests? #f ;no "check" target
        #:phases
        (modify-phases %standard-phases
         (delete 'configure)
         (replace 'build
                  (lambda _
-                   (system* "make" "-f" "Makefile.std")
+                   (zero? (system* "make" "-f" "Makefile.std"))
                    ))                 
         (replace 'install
                   (lambda* (#:key outputs #:allow-other-keys)
                     (let ((bin (string-append (assoc-ref outputs "out")
                                               "/bin/")))
-                      (install-file "plink" bin)
+                      (install-file "plink2" bin)
                       #t))))))
     (inputs
      `(("zlib" ,zlib)
-       ("lapack" ,lapack)))
+       ("openblas" ,openblas)
+       ("atlas" ,atlas)
+       ("lapack" ,lapack)
+       ("gfortran" ,gfortran)
+       ))
     (native-inputs
      `(("unzip" ,unzip)))
     (home-page "https://www.cog-genomics.org/plink2")

plink-ng-Makefile-zlib.patch

@@ -1,13 +1,126 @@
 diff --git a/Makefile.std b/Makefile.std
-index 95b0940..630188a 100644
+index 95b0940..30206be 100644
 --- a/Makefile.std
 +++ b/Makefile.std
-@@ -22,7 +22,7 @@ endif
- CFLAGS=-Wall -O2
- BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
- LINKFLAGS=-lm -lpthread
+@@ -1,62 +1,22 @@
+ # General-purpose Makefile for PLINK 1.90
+ #
+-# Compilation options:
+-#   Do not link to LAPACK                    NO_LAPACK
+ 
+-# Leave blank after "=" to disable; put "= 1" to enable
+-# (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h)
+-NO_LAPACK =
+-
+-
+-# should autodetect system
+-SYS = UNIX
+-ifdef SystemRoot
+-  SYS = WIN
+-else
+-  UNAME := $(shell uname)
+-  ifeq ($(UNAME), Darwin)
+-    SYS = MAC
+-  endif
+-endif
+-
+-CFLAGS=-Wall -O2
+-BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
+-LINKFLAGS=-lm -lpthread
 -ZLIB=zlib-1.2.8/libz.so.1.2.8
+-
+-ifeq ($(SYS), MAC)
+-  GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300)
+-  ifeq "$(GCC_GTEQ_43)" "1"
+-    CFLAGS=-Wall -O2 -flax-vector-conversions
+-  endif
+-  BLASFLAGS=-framework Accelerate
+-  LINKFLAGS=
+-  ZLIB=zlib-1.2.8/libz.1.2.8.dylib
+-endif
+-
+-ifeq ($(SYS), WIN)
+-# Note that, unlike the Linux and Mac build processes, this STATICALLY links
+-# LAPACK, since we have not gotten around to trying dynamically-linked LAPACK
+-# on Windows.
+-# If you don't already have LAPACK built, you'll probably want to turn on
+-# NO_LAPACK.
+-  BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a
+-  LINKFLAGS=-lm -static-libgcc
+-  ZLIB=zlib-1.2.8/libz.a
+-endif
+-
+-ifdef NO_LAPACK
+-  BLASFLAGS=
+-endif
++# CFLAGS=-Wall -O2
++# BLASFLAGS=-lblas -llapack -latlas
++LINKFLAGS=-lm -lpthread -lopenblas -llapack -latlas -lstdc++
 +ZLIB=-lz 
  
- ifeq ($(SYS), MAC)
-   GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300)
+ SRC = plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c
+ 
++OBJ = plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o
++
+ # In the likely event that you are concurrently using PLINK 1.07, we suggest
+ # either renaming that binary to "plink1" or this one to "plink2".
+ 
+-plink: $(SRC)
+-	g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
++# plink: $(SRC)
++# 	g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
+ 
+-plinkw: $(SRC)
++plink: $(SRC)
+ 	g++ $(CFLAGS) $(SRC) -c
+-	gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
++	gfortran $(OBJ) -o plink2 $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
++	# gfortran $^ -o plink2 -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
+diff --git a/dose2plink.c b/dose2plink.c
+index dc1f33a..ca2d31c 100644
+--- a/dose2plink.c
++++ b/dose2plink.c
+@@ -96,7 +96,7 @@
+   #endif
+ #endif
+ 
+-#include "zlib-1.2.8/zlib.h"
++#include "zlib.h"
+ 
+ #ifdef __APPLE__
+   #include <sys/sysctl.h>
+diff --git a/pigz.c b/pigz.c
+index 6605925..3f4ca54 100644
+--- a/pigz.c
++++ b/pigz.c
+@@ -303,7 +303,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <windows.h>
+-#include "zlib-1.2.8/zlib.h"
++#include "zlib.h"
+ 
+ void pigz_init(uint32_t setprocs) {
+   return;
+@@ -383,7 +383,7 @@ void parallel_compress(char* out_fname, uint32_t do_append, uint32_t(* emitn)(ui
+ #  include <sys/pstat.h>
+ #endif
+ 
+-#include "zlib-1.2.8/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
++#include "zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
+                         /* deflateEnd(), deflateSetDictionary(), crc32(),
+                            inflateBackInit(), inflateBack(), inflateBackEnd(),
+                            Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY,
+diff --git a/plink_common.h b/plink_common.h
+index 5dd77e8..4da9371 100644
+--- a/plink_common.h
++++ b/plink_common.h
+@@ -139,7 +139,7 @@
+ 
+ #endif // __LP64__
+ 
+-#include "zlib-1.2.8/zlib.h"
++#include "zlib.h"
+ #include "SFMT.h"
+ 
+ // 64MB of non-workspace memory guaranteed for now