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| author | Efraim Flashner | 2019-06-21 06:09:44 -0500 |
|---|---|---|
| committer | Efraim Flashner | 2019-06-21 06:43:37 -0500 |
| commit | dae92276b5955783ceea8480dd2ece4263a54520 (patch) | |
| tree | 5ef462ebc4fa39b67c4ccec09a5758e836b2b592 | |
| parent | 73227ba7193a191bea7a11bd3fecea91c60bd01b (diff) | |
| download | guix-bioinformatics-dae92276b5955783ceea8480dd2ece4263a54520.tar.gz | |
fixup hyphy package definition
| -rw-r--r-- | gn/packages/hyphy.scm | 40 |
1 files changed, 10 insertions, 30 deletions
diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm index e5c120a..1a34c98 100644 --- a/gn/packages/hyphy.scm +++ b/gn/packages/hyphy.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com> +;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -19,28 +20,11 @@ (define-module (gn packages hyphy) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) - #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix packages) #:use-module (gnu packages algebra) - #:use-module (gnu packages autotools) - #:use-module (gnu packages curl) - #:use-module (gnu packages gawk) - #:use-module (gnu packages cmake) - #:use-module (gnu packages boost) - #:use-module (gnu packages glib) - #:use-module (gnu packages image) - #:use-module (gnu packages video) - #:use-module (gnu packages textutils) - #:use-module (gnu packages gl) - #:use-module (gnu packages pkg-config) - #:use-module (gnu packages maths) - #:use-module (gnu packages web) - #:use-module (gnu packages databases) - #:use-module (gnu packages python) - #:use-module (gnu packages xorg) - #:use-module (gnu packages version-control) - #:use-module (gnu packages linux)) + #:use-module (gnu packages mpi) + #:use-module (gnu packages python)) (define-public hyphy ; guix: check (package @@ -48,7 +32,7 @@ (version "2.2.6") (source (origin (method url-fetch) - (uri (string-append "https://github.com/veg/hyphy/archive/" version + (uri (string-append "https://github.com/veg/hyphy/archive/" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 @@ -56,16 +40,15 @@ "00i3609nywb1xfq50p3kvfbvahql241ciq23jrf67z0yp4y5l5a9")))) (inputs `(("python" ,python-2) + ("openmpi" ,openmpi) ("fftw-openmpi" ,fftw-openmpi))) (build-system cmake-build-system) (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "make" "MPI"))))))) - (arguments - `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") - #:tests? #f)) + '(#:make-flags '("MPI") + #:configure-flags (list "-DCMAKE_BUILD_TYPE=Release" + (string-append "-DINSTALL_PREFIX=" + (assoc-ref %outputs "out"))) + #:tests? #f)) (synopsis "hyphy: an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.") @@ -79,6 +62,3 @@ interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R. ") (home-page "http://hyphy.org") (license license:expat))) - - - |