;; To use this file to build HEAD of gemma:
;;
;;   guix build -f guix.scm       # default builds pangemma-git
;;   guix build -L . gemma-git    # builds original (still)
;;
;; To get a development container (e.g., run in emacs shell).
;;
;;   guix shell -C -D -F -v 3 -L . pangemma-shell-git  # pangemma-shell-git
;;
;;   see premake5.lua header for examples.
;;
;;   guix shell -C -D -F -v 3 -L . gemma-git           # for specific packages
;;

(define-module (guix)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix gexp)
  #:use-module (guix packages)
  #:use-module (guix git-download)
  #:use-module (guix build-system gnu)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages base)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages commencement)
  #:use-module (gnu packages check)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages gdb)
  #:use-module (gnu packages guile)
  #:use-module (gnu packages guile-xyz)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages ruby)
  #: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 describe --always --tags --long|tr -d $'\n'" OPEN_READ)))

(define %pangemma-version
    (read-string (open-pipe "cat VERSION|tr -d $'\n'" OPEN_READ)))

(define-public pangemma-base-git
  "Pangemma base build package"
  (package
    (name "pangemma-git")
    (version (git-version %pangemma-version "HEAD" %git-commit))
    (source (local-file %source-dir #:recursive? #t))
    (build-system gnu-build-system)
    (inputs
     (list gsl
           openblas
           guile-3.0
           `(,guile-3.0 "debug")
           guile-lmdb
           lmdb
           ninja
           ruby
           zlib))
    (propagated-inputs
     (list
      `("guile" ,guile-3.0-latest)
      `("guile-debug" ,guile-3.0-latest "debug")))

    ;; ("gsl-static" ,gsl-static)
    ;; ("zlib:static" ,zlib "static")
    (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://git.genenetwork.org/pangemma/")
    (synopsis "Tool for genome-wide efficient mixed model association")
    (description "New version of Genome-wide Efficient Mixed Model Association (PANGEMMA)
provides a standard linear mixed model resolver with application in
genome-wide association studies (GWAS).")
    (license license:gpl3)))

(define-public pangemma-shell-git
  "Shell version for development"
  (package
    (inherit pangemma-base-git)
    (name "pangemma-shell-git")
    (build-system gnu-build-system)
    (propagated-inputs
     (modify-inputs (package-inputs pangemma-base-git)
                    (append which binutils coreutils gcc-toolchain premake5 gnu-make ;; for the shell
                 )))
    (arguments
     `(#:phases (modify-phases %standard-phases
                               (delete 'configure)
                               (delete 'build)
                               (delete 'package)
                               (delete 'check)
                               (delete 'install))))
    (description "Pangemma shell for development")
    ))

;; ---- legacy build -----------------------------------------------------------------
(define-public gemma-git
  "Original legacy gemma -- for as long as it compiles"
  (package
    (name "gemma-git")
    (version (git-version %pangemma-version "HEAD" %git-commit))
    (source (local-file %source-dir #:recursive? #t))
    (build-system gnu-build-system)
    (inputs
     (list catch2
           gdb
           gsl
           openblas
           zlib))
       ;; ("gsl-static" ,gsl-static)
       ;; ("zlib:static" ,zlib "static")
    (native-inputs ; for running tests
     (list perl 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).")
    (license license:gpl3)))



gemma-git