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authorEfraim Flashner2019-08-15 06:21:37 -0500
committerEfraim Flashner2019-08-15 06:42:52 -0500
commitd7aeb9658caefed71d901acbdd09cd3774ea4fbc (patch)
tree21084cdf6c52bf659c74ea923da6180c862508a7 /gn/packages
parentc95495b1abfd6d0ed610a27e925c3cb6d5776dbf (diff)
downloadguix-bioinformatics-d7aeb9658caefed71d901acbdd09cd3774ea4fbc.tar.gz
gn: hyphy: Update to 2.5.0.
* gn/packages/hyphy.scm (hyphy): Update to 2.5.0. [source]: Download using 'git-fetch'. [inputs]: Add curl, openssl. [arguments]: Add test-target.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/hyphy.scm31
1 files changed, 19 insertions, 12 deletions
diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm
index 1a34c98..d0e9127 100644
--- a/gn/packages/hyphy.scm
+++ b/gn/packages/hyphy.scm
@@ -19,36 +19,43 @@
(define-module (gn packages hyphy)
#:use-module ((guix licenses) #:prefix license:)
- #:use-module (guix download)
+ #:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module (guix packages)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages curl)
#:use-module (gnu packages mpi)
- #:use-module (gnu packages python))
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages tls))
+;; TODO: Unbundle sqlite, gtest
(define-public hyphy ; guix: check
(package
(name "hyphy")
- (version "2.2.6")
+ (version "2.5.0")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/veg/hyphy/archive/" version
- ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/veg/hyphy.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "00i3609nywb1xfq50p3kvfbvahql241ciq23jrf67z0yp4y5l5a9"))))
+ "1fvmwg2rxkz3abhhldiir69vmyc4i85vdvy64bizgxd0g2k2bikm"))))
(inputs
- `(("python" ,python-2)
+ `(("curl" ,curl)
+ ("fftw-openmpi" ,fftw-openmpi)
("openmpi" ,openmpi)
- ("fftw-openmpi" ,fftw-openmpi)))
+ ("openssl" ,openssl)
+ ("python" ,python-2)))
(build-system cmake-build-system)
(arguments
- '(#:make-flags '("MPI")
+ '(#:make-flags '("MPI") ; Add "GTEST" for tests, currently fails to compile.
#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
(string-append "-DINSTALL_PREFIX="
(assoc-ref %outputs "out")))
- #:tests? #f))
+ #:tests? #f
+ #:test-target "HYPHYGTEST"))
(synopsis "hyphy: an open-source software package for the analysis
of genetic sequences using techniques in phylogenetics, molecular
evolution, and machine learning.")