From a36abbe00577dcec5fc3c9ec5bb797a1c1adb6a5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 13 Jan 2021 14:09:59 +0200 Subject: gnu: gemma: Update to 0.98.3. * gnu/packages/bioinformatics.scm (gemma): Update to 0.98.3. [source, home-page]: Update to new upstream URI. [inputs]: Remove eigen, gfortran, lapack. [arguments]: Remove make-flags. Remove 'find-eigen phase. Rename 'bin-mkdir phase to 'prepare-build and substitute openblas include directory. --- gnu/packages/bioinformatics.scm | 49 ++++++++++++++--------------------------- 1 file changed, 16 insertions(+), 33 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 512abcd8fd..8dcf2fd649 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016, 2020 Roel Janssen -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner +;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner ;;; Copyright © 2016, 2020 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice @@ -3563,56 +3563,39 @@ comment or quality sections.") (define-public gemma (package (name "gemma") - (version "0.98") + (version "0.98.3") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/xiangzhou/GEMMA") - (commit (string-append "v" version)))) + (url "https://github.com/genetics-statistics/GEMMA") + (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg")))) + "1p8a7kkfn1mmrg017aziy544aha8i9h6wd1x2dk3w2794wl33qb7")))) + (build-system gnu-build-system) (inputs - `(("eigen" ,eigen) - ("gfortran" ,gfortran "lib") - ("gsl" ,gsl) - ("lapack" ,lapack) + `(("gsl" ,gsl) ("openblas" ,openblas) ("zlib" ,zlib))) - (build-system gnu-build-system) (arguments - `(#:make-flags - '(,@(match (%current-system) - ("x86_64-linux" - '("FORCE_DYNAMIC=1")) - ("i686-linux" - '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")) - (_ - '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1")))) - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) - (add-after 'unpack 'find-eigen + (add-after 'unpack 'prepare-build (lambda* (#:key inputs #:allow-other-keys) - ;; Ensure that Eigen headers can be found - (setenv "CPLUS_INCLUDE_PATH" - (string-append (assoc-ref inputs "eigen") - "/include/eigen3")) + (mkdir-p "bin") + (substitute* "Makefile" + (("/usr/local/opt/openblas") + (assoc-ref inputs "openblas"))) #t)) - (add-before 'build 'bin-mkdir - (lambda _ - (mkdir-p "bin") - #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (install-file "bin/gemma" - (string-append - out "/bin"))) + (install-file "bin/gemma" + (string-append (assoc-ref outputs "out") "/bin")) #t))) #:tests? #f)) ; no tests included yet - (home-page "https://github.com/xiangzhou/GEMMA") + (home-page "https://github.com/genetics-statistics/GEMMA") (synopsis "Tool for genome-wide efficient mixed model association") (description "Genome-wide Efficient Mixed Model Association (GEMMA) provides a -- cgit v1.2.3