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authorEfraim Flashner <efraim@flashner.co.il>2021-01-13 14:09:59 +0200
committerEfraim Flashner <efraim@flashner.co.il>2021-01-14 20:43:30 +0200
commita36abbe00577dcec5fc3c9ec5bb797a1c1adb6a5 (patch)
tree19c1623a413e1351438a05212654bf2e79636d33
parentf79f41e2403e69e4ae5c57e2a5cbd348d8677a98 (diff)
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.
-rw-r--r--gnu/packages/bioinformatics.scm49
1 files 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 <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -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