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;; 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
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