Updated and fixed plink-nggn-stable

3 files changed, 24 insertions, 152 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c04c6c8..f62949d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -830,7 +830,7 @@ confidence region for the location of a putative QTL.")
         (replace 'build
                  (lambda _
                    (zero? (system* "make" "-f" "Makefile.std"))
-                   ))                 
+                   ))
         (replace 'install
                   (lambda* (#:key outputs #:allow-other-keys)
                     (let ((bin (string-append (assoc-ref outputs "out")
@@ -861,45 +861,46 @@ subsequent visualization, annotation and storage of results.")
     (license (list license:gpl2 license:lgpl2.1+))))
 
 (define-public plink-ng
-  (let ((commit "6ab6ecf81e904b7db76454422ea59baae437d961"))
+  (let ((commit "5d1db4313ba0cc976562da233db4aced78975d10"))
   (package
     (name "plink-ng")
-    (version (string-append "1.90b3-" commit ))
+    (version (string-append "1.90b3-" commit )) ; Aug 11, 2016
     (source (origin
              (method git-fetch)
              (uri (git-reference
-                   (url "https://github.com/chrchang/plink-ng.git")
+                   (url "https://github.com/genenetwork/plink-ng.git")
                    (commit commit)))
-             (file-name (string-append name "-" commit)) 
+             (file-name (string-append name "-" commit))
              (sha256
               (base32
-               "0djnfcr3lm6839lkglpq1p4w09zlgv68p618c2i5dng4jhwji94k"))))
-    ;;; (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch"))
+               "1366li3ks9076bblvd1rpzkjq4j8f8f08lhga4c1ckrkil3xww4m"))))
+            ;; no longer (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")))))
+    (inputs
+     `(("zlib" ,zlib)
+       ("openblas" ,openblas)
+       ;; ("atlas" ,atlas) ; openblas replaces atlas
+       ("lapack" ,lapack)  ; lapack is disabled in GUIX openblas
+       ;; ("gfortran" ,gfortran)
+       ;; ("python" ,python-2)   ;; for tests - currently disabled
+       ))
+    (native-inputs
+     `(("unzip" ,unzip)))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f ;no "check" target
+     '(#:tests? #f ;no "check" target. Some of the python-based tests fail
        #:phases
        (modify-phases %standard-phases
         (delete 'configure)
         (replace 'build
                  (lambda _
-                   (zero? (system* "make" "-f" "Makefile.std"))
-                   ))                 
+                   (zero? (system* "make" "-f" "Makefile.guix"))
+                   ))
         (replace 'install
                   (lambda* (#:key outputs #:allow-other-keys)
                     (let ((bin (string-append (assoc-ref outputs "out")
                                               "/bin/")))
                       (install-file "plink2" bin)
                       #t))))))
-    (inputs
-     `(("zlib" ,zlib)
-       ("openblas" ,openblas)
-       ;; ("atlas" ,atlas)
-       ;; ("lapack" ,lapack)
-       ("gfortran" ,gfortran)
-       ))
-    (native-inputs
-     `(("unzip" ,unzip)))
     (home-page "https://www.cog-genomics.org/plink2")
     (synopsis "Whole genome association analysis toolset")
     (description
@@ -922,7 +923,7 @@ subsequent visualization, annotation and storage of results.")
              (uri (git-reference
                    (url "https://github.com/genenetwork/GEMMA.git")
                    (commit commit)))
-             (file-name (string-append name "-" commit)) 
+             (file-name (string-append name "-" commit))
              (sha256
               (base32
                "1drffdgwbzgiw9sf55ghl3zjv58f8i9kfz0zys5mp6n06syp4ira"))))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 81873d5..a7317c6 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -163,8 +163,8 @@
               ("mysql" ,mysql)
               ("gemma" ,gemma-git)
               ("genenetwork2-files-small" ,genenetwork2-files-small)
+              ("plink-ng" ,plink-ng)
               ("pylmm-gn2" ,pylmm-gn2)
-              ;; ("plink2" ,plink-ng) disabled - FIXME
               ("nginx" ,nginx)
               ("python2-flask" ,python2-flask)
               ("python2-htmlgen-gn" ,python2-htmlgen-gn)
@@ -200,14 +200,14 @@
                       (let* (
                              (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))
                              (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
-                             ;; (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2"))
+                             (plink2cmd (string-append (assoc-ref inputs "plink-ng") "/bin/plink2"))
                              (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
                              )
 
                (substitute* '("etc/default_settings.py")
                             (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
                             (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
-                            ;; (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
+                            (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
                             (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
                             )
                ))))
diff --git a/plink-ng-Makefile-zlib-git.patch b/plink-ng-Makefile-zlib-git.patch
deleted file mode 100644
index 79986b8..0000000
--- a/plink-ng-Makefile-zlib-git.patch
+++ /dev/null
@@ -1,129 +0,0 @@
-diff --git a/Makefile.std b/Makefile.std
-index e204486..ca65bd3 100644
---- a/Makefile.std
-+++ b/Makefile.std
-@@ -1,64 +1,23 @@
- # 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 =
-+# CFLAGS=-Wall -O2
-+# BLASFLAGS=-lblas -llapack -latlas
-+LINKFLAGS=-lm -lpthread -lopenblas -llapack -latlas -lstdc++
-+ZLIB=-lz 
- 
-+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_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c
- 
--# 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 -ldl
--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 "$(GCC_GTEQ_43)" "1"
--    CFLAGS=-Wall -O2 -flax-vector-conversions
--  endif
--  BLASFLAGS=-framework Accelerate
--  LINKFLAGS=-ldl
--  ZLIB=zlib-1.2.8/libz.1.2.8.dylib
--endif
--
--ifeq ($(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
-+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_perm.o plink_rserve.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o Rconnection.o hfile.o bgzf.o
- 
--ifdef NO_LAPACK
--  BLASFLAGS=
--endif
- 
--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_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c
-+# 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".
- 
--# In the event that you are still concurrently using PLINK 1.07, we suggest
--# renaming that binary to "plink107" and "plink1".  (Previously,
--# "plink1"/"plink2" was suggested here; that also works for now, but it may
--# lead to minor problems when PLINK 2.0 is released.)
-+# plink: $(SRC)
-+# 	g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
- 
- plink: $(SRC)
--	g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
--
--plinkw: $(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 46b0525..3ce9a6b 100644
---- a/pigz.c
-+++ b/pigz.c
-@@ -297,7 +297,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <windows.h>
--#include "zlib-1.2.8/zlib.h"
-+#include "zlib.h"
- 
- #include "pigz.h"
- 
-@@ -513,7 +513,7 @@ int32_t flex_pzwrite_close_null(Pigz_state* ps_ptr, char* writep) {
- #  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 84eb929..e0b5cca 100644
---- a/plink_common.h
-+++ b/plink_common.h
-@@ -177,7 +177,7 @@
- #define VEC_BITS (VEC_BYTES * 8)
- #define VEC_BITS_M1 (VEC_BITS - 1)
- 
--#include "zlib-1.2.8/zlib.h"
-+#include "zlib.h"
- #include "SFMT.h"
- 
- // 64MB of non-workspace memory guaranteed for now.