guix-static.scm: Fixed building a static wfmash binary and libs. See …

…the header of the file for instructions.

guix-static.scm

@@ -10,7 +10,7 @@
 ;;
 ;;   mkdir build
 ;;   cd build
-;;   cmake ..
+;;   cmake -DBUILD_STATIC=1 ..
 ;;   make
 ;;
 ;; For the tests you may need /usr/bin/env. Inside the container:
@@ -21,18 +21,17 @@
 
 (use-modules
  ((guix licenses) #:prefix license:)
+  (guix build-system cmake)
+  (guix download)
   (guix gexp)
-  (guix packages)
   (guix git-download)
-  (guix build-system cmake)
-  ; (guix gexp)
+  (guix packages)
   (guix utils)
   (gnu packages algebra)
   (gnu packages base)
   (gnu packages bioinformatics)
   (gnu packages build-tools)
   (gnu packages compression)
-  ; (gnu packages curl)
   (gnu packages gcc)
   (gnu packages jemalloc)
   (gnu packages llvm)
@@ -45,12 +44,31 @@
   (ice-9 popen)
   (ice-9 rdelim))
 
+(define-public libdeflate-static
+  (package
+    (inherit libdeflate)
+    (name "libdeflate-static")
+    (version "1.19")
+    (arguments
+     (list #:configure-flags
+           #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=YES"
+                   "-DLIBDEFLATE_BUILD_TESTS=YES")))))
+
 ;; A minimal version of htslib that does not depend on curl and openssl. This
 ;; reduces the number of higher order dependencies in static linking.
 (define-public htslib-static
   (package
     (inherit htslib)
     (name "htslib-static")
+    (version "1.19")
+    (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://github.com/samtools/htslib/releases/download/"
+                  version "/htslib-" version ".tar.bz2"))
+            (sha256
+             (base32
+              "0dh79lwpspwwfbkmllrrhbk8nkvlfc5b5ib4d0xg5ld79w6c8lc7"))))
     (arguments
      (substitute-keyword-arguments (package-arguments htslib)
        ((#:configure-flags flags ''())
@@ -66,31 +84,35 @@
 (define-public wfmash-git
   (package
     (name "wfmash-git")
-    (version (git-version "0.10.7" "HEAD" %git-commit))
+    (version (git-version "0.21" "HEAD" %git-commit))
     (source (local-file %source-dir #:recursive? #t))
     (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+         ,#~(list "-DBUILD_STATIC=1" "-DCMAKE_INSTALL_RPATH=") ; force cmake static build and do not rewrite RPATH
+       #:tests? #f)) ; disable tests until I fix finding the binary wfmash
     (inputs
      `(
-       ;; ("clang" ,clang)      ; add this to test clang builds
-       ;; ("lld" ,lld)          ; add this to test clang builds
+       ("bzip2-static" ,bzip2 "static")    ; libz2 part of htslib for static builds
+       ("coreutils" ,coreutils) ; for echo and env in tests
        ("gcc" ,gcc-12)
-       ("gsl-static" ,gsl "static")
+       ("git" ,git)
        ("gmp" ,gmp)
+       ("gsl-static" ,gsl "static")
+       ("gsl" ,gsl)
+       ("htslib-static" ,htslib-static)
+       ("jemalloc" ,jemalloc)
+       ("libdeflate-static" ,libdeflate-static)
        ("make" ,gnu-make)
        ("pkg-config" ,pkg-config)
-       ("jemalloc" ,jemalloc)
-       ("htslib" ,htslib-static)
-       ("git" ,git)
-       ; ("bc" ,bc)               ; for tests
-       ("coreutils" ,coreutils) ; for echo and env in tests
-       ; ("curl" ,curl)
-       ; ("parallel" ,parallel) ; for wfmash-parallel
-       ("bzip2-static" ,bzip2 "static")    ; libz2 part of htslib for static builds
        ("xz-static" ,xz "static")     ; for static builds
        ("zlib-static" ,zlib "static")))
      (synopsis "wfmash")
      (description
-      "wfmash.")
+      "wfmash is an aligner for pangenomes that combines efficient homology
+mapping with base-level alignment. It uses MashMap to find approximate
+mappings between sequences, then applies WFA (Wave Front Alignment) to
+obtain base-level alignments.")
      (home-page "https://github.com/waveygang/wfmash")
      (license license:expat)))