guix.scm

;; To use this file to build a version of wfmash using git HEAD:
;;
;;   guix build -f guix.scm                  # default build
;;   guix build -L . wfmash-gcc-git          # stanard gcc build
;;   guix build -L . wfmash-gcc-debug-git    # gcc build with debug and ASAN
;;   guix build -L . wfmash-gcc-profile-git  # run the profiler!
;;   guix build -L . wfmash-static-gcc-git   # gcc static build (default)
;;   guix build -L . wfmash-clang-git        # clang build
;;
;; To get a development container using a recent guix (see `guix pull`)
;;
;;   guix shell -C -D -F -f guix.scm         # default build
;;   guix shell -L . -C -D -F wfmash-gcc-git # preferred development container
;;   guix shell -L . -C -D -F wfmash-gcc-static-git
;;   guix shell -L . -C -D -F wfmash-clang-git
;;
;; and inside the container
;;
;;   mkdir build
;;   cd build
;;   rm -rf ../build/*
;;   cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_OPTIMIZED=1 ..
;;   make -j 12 VERBOSE=1
;;   ctest . --verbose
;;
;; alternative builds
;;
;;   cmake -DCMAKE_BUILD_TYPE=Debug ..           # for development (use wfmash-gcc-git)
;;   cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ..  # for distros including Debian (use wfmash-gcc-git)
;;   cmake -DBUILD_STATIC=1 ..                   # static binary (use wfmash-gcc-static-git)
;;
;; list packages
;;
;;   guix package -L . -A|grep wfm
;;
;; Installing guix (note that Debian comes with guix). Once installed update as a normal user with:
;;
;;   mkdir ~/opt
;;   guix pull -p ~/opt/guix # update guix takes a while - don't do this often!
;;
;; Use the update guix to build wfmash:
;;
;;   ~/opt/guix/bin/guix build -f guix.scm
;;
;; Or get a shell
;;
;;   ~/opt/guix/gin/guix build -f guix.scm
;;
;; If things do not work you may also have to update the guix-daemon in systemd. Guix mostly downloads binary
;; substitutes. If it wants to build a lot of software you probably have substitutes misconfigured.

;; by Pjotr Prins & Andrea Guarracino (c) 2023-2024

(define-module (guix)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix build-system cmake)
  #:use-module (guix download)
  #:use-module (guix gexp)
  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cpp)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages jemalloc)
  #:use-module (gnu packages linux) ; for util-linux column
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages version-control)
  #:use-module (srfi srfi-1)
  #:use-module (ice-9 popen)
  #:use-module (ice-9 rdelim))

(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 wfmash-base-git
  (package
    (name "wfmash-base-git")
    (version (git-version "0.21" "HEAD" %git-commit))
    (source (local-file %source-dir #:recursive? #t))
    (build-system cmake-build-system)
    (inputs
     `(
       ("bash" ,bash) ; for testing
       ("bedtools" ,bedtools) ; for testing
       ("util-linux" ,util-linux) ; for testing
       ("samtools" ,samtools) ; for testing
       ("bzip2" ,bzip2)
       ("coreutils" ,coreutils) ; for echo and env in tests
       ("git" ,git)
       ("gmp" ,gmp)
       ("gsl" ,gsl)
       ("htslib" ,htslib)
       ("jemalloc" ,jemalloc)
       ("libdeflate" ,libdeflate)
       ("make" ,gnu-make)
       ("pkg-config" ,pkg-config)
       ("xz" ,xz)
       ("zlib" ,zlib)))
     (synopsis "wfmash")
     (description
      "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)))

(define-public wfmash-gcc-git
  "Default build with gcc - as is used in distros"
  (package
    (inherit wfmash-base-git)
    (name "wfmash-gcc-git")
    (version (git-version "0.21" "HEAD" %git-commit))
    (inputs
     (modify-inputs (package-inputs wfmash-base-git)
         (append gcc-14
                 )))
    ))

(define-public wfmash-gcc-debug-git
  "Build with debug options"
  (package
    (inherit wfmash-gcc-git)
    (name "wfmash-gcc-debug-git")
    (version (git-version "0.21" "HEAD" %git-commit))
    (arguments
     `(;; #:tests? #f ;; skip tests, this is mostly to run a shell
       #:configure-flags
       ,#~(list
           "-DASAN=ON"
           "-DDISABLE_LTO=ON"
           "-DCMAKE_BUILD_TYPE=Debug"))) ; force cmake static build and do not rewrite RPATH
    (inputs
     (modify-inputs (package-inputs wfmash-gcc-git)
         (append gperftools
                 )))
    ))

(define-public wfmash-clang-git
  "Clang+LLVM build"
  (package
    (inherit wfmash-base-git)
    (name "wfmash-clang-git")
    (version (git-version "0.21" "HEAD" %git-commit))
    (inputs
     (modify-inputs (package-inputs wfmash-base-git)
         (append clang-toolchain-18
                 lld
                 libomp
                 )))
    ))

(define-public wfmash-gcc-profile-git
  "Build wfmash optimally and automatically run profiler on all tests"
  (package
    (inherit wfmash-gcc-git)
    (name "wfmash-gcc-profile-git")
    (version (git-version "0.21" "HEAD" %git-commit))
    (arguments
     `(#:tests? #f ;; running tests as profiler
       #:configure-flags
         ,#~(list
             "-DCMAKE_BUILD_TYPE=Release"
             "-DBUILD_OPTIMIZED=ON"
             "-DPROFILER=ON")
       #:phases
         ,#~(modify-phases %standard-phases
            (add-after 'install 'run-profiler-on-all2all
                       (lambda* (#:key outputs #:allow-other-keys)
                         (invoke "ctest" "--verbose" "-R" "all2all") ; only run all2all test
                         (invoke "ls" "-l" "bin/wfmash")
                         (invoke "ls" "-l")
                         (invoke "pprof" "--text" "bin/wfmash" "wfmash.prof")
                         (mkdir-p (string-append #$output:doc "/share")))))))
    (inputs
     (modify-inputs (package-inputs wfmash-gcc-git)
                    (append gperftools
                            coreutils ;; for ls
                 )))
    ))

;; ==== The following is for static binary builds using gcc - used mostly for deployment ===

;; Guix does not come with a static version of libdeflate
(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 static 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 ''())
        ''())))
    (inputs
     (list bzip2 xz))))

(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 wfmash-static-gcc-git
  "Optimized for latest AMD architecture build and static deployment.
These binaries can be copied to HPC."
  (package
    (inherit wfmash-base-git)
    (name "wfmash-static-gcc-git")
    (version (git-version "0.21" "HEAD" %git-commit))
    (arguments
     `(;; #:tests? #f
       #:configure-flags
       ,#~(list
           "-DBUILD_STATIC=ON"
           "-DBUILD_OPTIMIZED=ON"
           "-DCMAKE_BUILD_TYPE=Release"
           "-DCMAKE_INSTALL_RPATH="))) ; force cmake static build and do not rewrite RPATH
    (inputs
     (modify-inputs (package-inputs wfmash-gcc-git)
                    (prepend
                     `(,bzip2 "static")
                     `(,zlib "static")
                     `(,gsl "static")
                     `(,xz "static")
                     libdeflate-static
                     htslib-static
                     )))))

wfmash-static-gcc-git ;; default optimized static deployment build