Makefile and guix: build default sambamba

Makefile

@@ -42,6 +42,7 @@ endif
 BIOD_PATH=./BioD:./BioD/contrib/msgpack-d/src
 DFLAGS      = -wi -I. -I$(BIOD_PATH) -g -J.
 LDFLAGS     = -L=-flto=full
+PREFIX      = /usr/local
 
 # DLIBS       = $(LIBRARY_PATH)/libphobos2-ldc.a $(LIBRARY_PATH)/libdruntime-ldc.a
 # DLIBS_DEBUG = $(LIBRARY_PATH)/libphobos2-ldc-debug.a $(LIBRARY_PATH)/libdruntime-ldc-debug.a
@@ -117,7 +118,7 @@ debug-strip:
 pgo-static: static debug-strip
 
 install:
-	install -m 0755 $(OUT) $(prefix)/bin
+	install -m 0755 $(OUT) $(PREFIX)/bin
 
 clean: clean-d
 	rm -f profile.data

guix.scm

@@ -1,11 +1,10 @@
-;; To get a development container (inside emacs shell will work)
+;; To build sambamba using a recent Guix:
 ;;
-;;   guix shell -C -D -f guix.scm -- bash --init-file <(echo "ln -s /bin/sh /bin/bash")
+;;   guix build -f guix.scm
 ;;
-;; For the tests you may need /usr/bin/env. In a container create it with
-;;
-;;   mkdir -p /usr/bin ; ln -s $GUIX_ENVIRONMENT/bin/env /usr/bin/env
+;; To get a development container (inside emacs shell will work!)
 ;;
+;;   guix shell -C -D -F -f guix.scm
 
 (use-modules
   (srfi srfi-1)
@@ -14,91 +13,86 @@
   ((guix licenses) #:prefix license:)
   (guix packages)
   (guix utils)
-  (guix download)
+  ;; (guix download)
   (guix git-download)
   (guix build-system gnu)
   (guix gexp)
   (gnu packages base)
+  (gnu packages bash)
   (gnu packages bioinformatics) ; for samtools in sambamba
   (gnu packages build-tools) ; for meson
   (gnu packages compression)
-  (gnu packages curl)
+  ;; (gnu packages curl)
   (gnu packages dlang)
   (gnu packages gcc)
   (gnu packages pkg-config)
-  (gnu packages perl)
+  ;; (gnu packages perl)
   (gnu packages python)
-  (gnu packages ninja)
-  (gnu packages ruby)
+  ;; (gnu packages ninja)
+  ;; (gnu packages ruby)
   (gnu packages tls)
   (gnu packages version-control)
   )
 
-#!
- (use-modules
-  (guix build-system cmake)
-  (guix utils)
-  (gnu packages base)
-  (gnu packages compression)
-  (gnu packages build-tools)
-  (gnu packages commencement) ; gcc-toolchain
-  (gnu packages curl)
-  (gnu packages datastructures)
-  (gnu packages gdb)
-  (gnu packages gcc)
-  (gnu packages jemalloc)
-  (gnu packages libffi)
-  (gnu packages mpi)
-  (gnu packages python)
-  (gnu packages python-xyz)
-  (gnu packages pkg-config)
-  (gnu packages tls)
-)
-
-!#
-
 (define %source-dir (dirname (current-filename)))
 
 (define %git-commit
   (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ)))
 
 (define-public sambamba-git
+  "singleobj -wi -I. -I./BioD:./BioD/contrib/msgpack-d/src -g -J. -O3 -release -enable-inlining -boundscheck=off"
   (package
     (name "sambamba-git")
     (version (git-version "1.0.0" "HEAD" %git-commit))
     (source (local-file %source-dir #:recursive? #t))
-      (build-system gnu-build-system)
-      (outputs '("out"     ; disable all checks for speed
-                 "debug"))
-      (inputs
-       `(("samtools" ,samtools) ; for pileup
-         ("bcftools" ,bcftools) ; for pileup
-         ("meson" ,meson) ; for testing meson build system
-         ("ninja" ,ninja)
-         ("pkg-config" ,pkg-config)
-         ("lz4" ,lz4)
-         ("lz4-static" ,lz4 "static")
-         ("zlib-static" ,zlib "static")
-         ("zlib" ,zlib) ; also for the static build we need the includes
-         ; ("zstd-lib" ,zstd "static")
-         ; ("zstd" ,zstd "lib") ; same
+    (build-system gnu-build-system)
+    (arguments
+     `(;; #:tests? #f  ;; we'll run tests
+       #:make-flags
+       (list
+        "VERBOSE=1"
+        (string-append "CC=" ,(cc-for-target))
+        (string-append "PREFIX=" %output))
+       #:phases
+       (modify-phases %standard-phases
+                      (delete 'configure)         ; no configure script
+                      (add-before 'check 'patch-tests
+                                  (lambda _
+                                    (substitute* "contrib/shunit2-2.0.3/shunit2"
+                                                 (("/bin/sh") (which "sh")))))
+                      (add-before 'install 'make-bin-dir
+                                  (lambda _
+                                    (mkdir-p (string-append %output "/bin"))))
+       )))
+    (outputs '("out"     ; disable all checks for speed
+               "debug"))
+    (inputs
+     `(("samtools" ,samtools) ; for pileup
+       ("bcftools" ,bcftools) ; for pileup
+       ;; ("meson" ,meson) ; for testing meson build system
+       ;; ("ninja" ,ninja)
+       ("pkg-config" ,pkg-config)
+       ("lz4-static" ,lz4 "static")
+       ("lz4" ,lz4)
+       ("zlib-static" ,zlib "static")
+       ("zlib" ,zlib) ; also for the static build we need the includes
+       ;; ("zstd-lib" ,zstd "static")
+       ;; ("zstd" ,zstd "lib") ; same
+       ))
+    (native-inputs
+     `(("ldc" ,ldc)
+       ("bash-minimal" ,bash-minimal) ; for sh in shunit2
+       ("python" ,python) ; Needed for building htslib and sambamba
+       ("which" ,which)
        ))
-      (native-inputs
-       `(("ldc" ,ldc)
-         ("coreutils" ,coreutils) ; for env
-         ; ("perl" ,perl) ; Needed for building htslib
-         ; ("ruby" ,ruby) ; Needed for building htslib
-         ("python" ,python) ; Needed for building htslib and sambamba
-         ("gcc" ,gcc)
-         ("which" ,which)))
-      (home-page "https://github.com/lomereiter/sambamba")
-      (synopsis "Fast tool for working with SAM and BAM files written in D.")
-      (description
-       "Sambamba is a high performance modern robust and fast
+    (home-page "https://github.com/BioD/sambamba")
+    (synopsis "Fast tool for working with SAM and BAM files written in D.")
+    (description
+     "Sambamba is a high performance modern robust and fast
 tool (and library), written in the D programming language, for working
 with SAM and BAM files.  Current parallelised functionality is
 an important subset of samtools functionality, including view, index,
 sort, markdup, and depth.")
-      (license license:gpl2+)))
+    (license license:gpl2+)))
 
 sambamba-git