Fix (guix.scm) build

1 files changed, 66 insertions, 141 deletions

diff --git a/guix.scm b/guix.scm
index 7440c81..9550be4 100644
--- a/guix.scm
+++ b/guix.scm
@@ -1,4 +1,4 @@
-;; To use this file to build HEAD of gemma:
+;; To use this file to build HEAD of pangemma:
 ;;
 ;;   guix build -f guix.scm
 ;;
@@ -12,26 +12,15 @@
   (guix gexp)
   (guix packages)
   (guix git-download)
+  (guix build-system copy)
   (guix build-system gnu)
   (guix utils)
-  (gnu packages algebra)
-  (gnu packages base)
   (gnu packages compression)
-  (gnu packages bioinformatics)
   (gnu packages build-tools)
-  (gnu packages check)
-  (gnu packages curl)
-  (gnu packages gcc)
-  (gnu packages gdb)
-  (gnu packages llvm)
+  (gnu packages databases)
+  (gnu packages guile)
   (gnu packages maths)
-  (gnu packages ninja)
-  (gnu packages parallel)
-  (gnu packages perl)
-  ;; (gnu packages perl6)
-  (gnu packages ruby)
   (gnu packages pkg-config)
-  ;; (gnu packages shell)  ;; for shunit2
   (srfi srfi-1)
   (ice-9 popen)
   (ice-9 rdelim))
@@ -39,140 +28,76 @@
 (define %source-dir (dirname (current-filename)))
 
 (define %git-commit
-    (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ)))
+    (string-trim-right (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ))))
 
-(define %gemma-version
-    (read-string (open-pipe "cat VERSION" OPEN_READ)))
+(define %pangemma-version
+    (string-trim-right (read-string (open-pipe "cat VERSION" OPEN_READ))))
 
-(define-public openblas-pangemma
+(define-public lmdbxx
+  (let ((commit "6f497d1d8e1a6e0afa8ae83891d13b3fac68b62c")
+        (revision "0"))
+    (package
+      (name "lmdbxx")
+      (version (git-version "1.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/hoytech/lmdbxx")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "1www519kfm0lq4g79i8hpfydwnfrf6p21fqrqcfl2sv072rghygj"))))
+      (build-system copy-build-system)
+      (arguments
+       (list #:install-plan
+             #~'(("include/lmdbxx/lmdb++.h" "include/lmdb++.h"))))
+      (home-page "https://github.com/hoytech/lmdbxx")
+      (synopsis "C++17 wrapper for the LMDB database library")
+      (description "Header-only C++17 wrapper for the LMDB embedded
+key-value store, with string_view-based API.")
+      (license license:unlicense))))
+
+(define-public pangemma-git
   (package
-    (name "openblas-pangemma")
-    (version "0.3.21")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/xianyi/OpenBLAS")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0yx1axiki12y0xz0d5s76vvl7ds36k0npv1sww08k2qslhz1g9qp"))))
+    (name "pangemma-git")
+    (version (git-version %pangemma-version "HEAD" %git-commit))
+    (source (local-file %source-dir #:recursive? #t))
     (build-system gnu-build-system)
-    (properties `((tunable? . #t)))
+    (inputs
+     (list gsl
+           guile-3.0
+           lmdb
+           openblas
+           zlib))
+    (native-inputs
+     (list lmdbxx
+           pkg-config
+           premake5))
     (arguments
      (list
-      #:tests? #f ;; skip tests
-      #:test-target "test"
-      ;; No default baseline is supplied for powerpc-linux.
-      #:substitutable? (not (target-ppc32?))
-      #:make-flags
-      #~(list (string-append "PREFIX=" #$output)
-              (string-append "CFLAGS=-O3 -g -Wno-incompatible-pointer-types -Wno-error=implicit-function-declaration")
-              "COPT="
-              "COMMON_OPT="
-              "DYNAMIC_ARCH="
-              "SHELL=bash"
-              "MAKE_NB_JOBS=0"          ;use jobserver for submakes
-
-              ;; This is the maximum number of threads OpenBLAS will ever use (that
-              ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
-              ;; is used.)  If we don't set it, the makefile sets it to the number
-              ;; of cores of the build machine, which is obviously wrong.
-              "NUM_THREADS=128"
-
-              ;; DYNAMIC_ARCH is only supported on some architectures.
-              ;; DYNAMIC_ARCH combined with TARGET=GENERIC provides a library
-              ;; which uses the optimizations for the detected CPU.  This can
-              ;; be overridden at runtime with the environment variable
-              ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU
-              ;; type.  On other architectures we target only the baseline CPU
-              ;; supported by Guix.
-              #$@(cond
-                    ((or (target-x86-64?)
-                         (target-x86-32?)
-                         (target-ppc64le?)
-                         (target-aarch64?))
-                     ;; Dynamic older enables a few extra CPU architectures
-                     ;; on x86_64 that were released before 2010.
-                     '("DYNAMIC_ARCH=1" "TARGET=GENERIC"))
-                     ;; '("DYNAMIC_ARCH=" "TARGET_CORE=ZEN"))
-                    ;; On some of these architectures the CPU type can't be detected.
-                    ;; We list the oldest CPU core we want to have support for.
-                    ;; On MIPS we force the "SICORTEX" TARGET, as for the other
-                    ;; two available MIPS targets special extended instructions
-                    ;; for Loongson cores are used.
-                    ((target-mips64el?)
-                     '("TARGET=SICORTEX"))
-                    ((target-arm32?)
-                     '("TARGET=ARMV7"))
-                    ((target-riscv64?)
-                     '("TARGET=RISCV64_GENERIC"))
-                    (else '())))
-      ;; no configure script
+      #:tests? #f ; tests need test data and ruby
       #:phases
       #~(modify-phases %standard-phases
           (delete 'configure)
-          (add-before 'build 'set-extralib
-            (lambda* (#:key inputs #:allow-other-keys)
-              ;; Get libgfortran found when building in utest.
-              (setenv "FEXTRALIB"
-                      (string-append
-                       "-L"
-                       (dirname
-                        (search-input-file inputs "/lib/libgfortran.so")))))))))
-    (inputs
-     (list `(,gfortran "lib")))
-    (native-inputs
-     (list cunit gfortran perl))
-    (home-page "https://www.openblas.net/")
-    (synopsis "Optimized BLAS library based on GotoBLAS")
-    (description
-     "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
-    (license license:bsd-3)))
-
-
-(define-public gemma-git
-  (package
-    (name "gemma-git")
-    (version (git-version "0.98.5" "HEAD" %git-commit))
-    (source (local-file %source-dir #:recursive? #t))
-    (build-system gnu-build-system)
-    (inputs
-     `(
-       ("catch" ,catch2)
-       ("gdb" ,gdb)
-       ;; ("gsl-static" ,gsl-static)
-       ("gsl" ,gsl)
-       ("openblas" ,openblas-pangemma)
-       ("ruby" ,ruby) ;; for testing
-       ("zlib:static" ,zlib "static")
-       ("zlib" ,zlib)))
-
-    (native-inputs ; for running tests
-     `(("perl" ,perl)
-       ("which" ,which)
-       ))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-                      (delete 'configure)
-                      (delete 'validate-runpath)
-                      (add-before 'build 'bin-mkdir
-                                  (lambda _
-                                    (mkdir-p "bin")
-                                    ))
-                      (replace 'install
-                               (lambda* (#:key outputs #:allow-other-keys)
-                                 (let ((out (assoc-ref outputs "out")))
-                                   (install-file "bin/gemma" (string-append out "/bin"))))))
-       #:tests? #t
-       #:parallel-tests? #f))
-    (home-page "https://github.com/genetics-statistics")
-    (synopsis "Tool for genome-wide efficient mixed model association")
-    (description "Genome-wide Efficient Mixed Model Association (GEMMA)
-provides a standard linear mixed model resolver with application in
-genome-wide association studies (GWAS).")
+          (replace 'build
+            (lambda _
+              (invoke "premake5" "gmake")
+              (invoke "make" "verbose=1" "config=release" "gemma"
+                      (string-append "CXXFLAGS=-std=c++17"
+                                     " -I" #$(this-package-native-input "lmdbxx") "/include"
+                                     " -I" #$(this-package-input "lmdb") "/include")
+                      (string-append "-j" (number->string
+                                            (parallel-job-count))))))
+          (replace 'install
+            (lambda _
+              (install-file "build/bin/Release/gemma"
+                            (string-append #$output "/bin")))))))
+    (home-page "https://github.com/genetics-statistics/pangemma")
+    (synopsis "Pangenome-enabled GEMMA for genome-wide association studies")
+    (description "PanGemma is a pangenome-enabled version of GEMMA
+(Genome-wide Efficient Mixed Model Association) for genome-wide association
+studies (GWAS) with support for LMDB-backed genotype storage and Guile
+scripting.")
     (license license:gpl3)))
 
-gemma-git
+pangemma-git