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authorPjotr Prins2019-08-01 08:59:33 -0500
committerPjotr Prins2019-08-01 08:59:33 -0500
commita5a1e75c1379d9c26c0a0f9dbb9fb069c7bf7f18 (patch)
tree198824fa4435adb7bc850f129fff600d607eaa22 /gn/packages/hyphy.scm
parentfd06a7a744cb2368d410e131b4f8c6bc7738cc94 (diff)
parent25db4463972bc8729436d84d8be003ea7eacad71 (diff)
downloadguix-bioinformatics-a5a1e75c1379d9c26c0a0f9dbb9fb069c7bf7f18.tar.gz
Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics
Diffstat (limited to 'gn/packages/hyphy.scm')
-rw-r--r--gn/packages/hyphy.scm40
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)))
-
-
-