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authorpjotrp2017-10-25 10:17:38 +0000
committerpjotrp2017-10-25 10:17:38 +0000
commit0a1882996472282dcf60f6a294a4f934d40d5bad (patch)
treea585598d7009902721feda6429e5aa1541cacaec /gn/packages
parent248b55f90f505394d884cdd80317db82e66d6d61 (diff)
downloadguix-bioinformatics-0a1882996472282dcf60f6a294a4f934d40d5bad.tar.gz
Updated GEMMA git
Added python-rpy2 since it got dropped from main
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/gemma.scm8
-rw-r--r--gn/packages/python.scm41
2 files changed, 45 insertions, 4 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index ff0a486..4e61beb 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -86,19 +86,19 @@ numbers.")
(define-public gemma-git-gn2 ; guix candidate
- (let ((commit "ffc99d62013b1a5025b21cc385dd9892360ebe49"))
+ (let ((commit "715b1c321d9aa7c5eb243982afc3f698e39ce8bc"))
(package
(name "gemma-git-gn2")
(version (string-append "0.97.2-gn2-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/genetics-statistics/GEMMA")
+ (url "https://github.com/genenetwork/GEMMA")
(commit commit)))
- (file-name (string-append name "-" version))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0v68p469a5x8m0sdh408zbxc8gqb5ysqpp5hvh8h51sjf8lwyxv6"))))
+ "1masl1h4l851aipzwd1jh7kbs28aizjla4dlv8hzvv0h2ir742h0"))))
(inputs `(
("gsl" ,gsl)
("eigen" ,eigen)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index f9bb733..9d85892 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -42,6 +42,47 @@
#:use-module (srfi srfi-1))
+(define-public python2-rpy2
+ (package
+ (name "python2-rpy2")
+ (version "2.7.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "rpy2" version))
+ (sha256
+ (base32
+ "0nhan2qvrw7b7gg5zddwa22kybdv3x1g26vkd7q8lvnkgzrs4dga"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ ;; It's easier to run tests after install.
+ ;; Make installed package available for running the tests
+ (add-installed-pythonpath inputs outputs)
+ (zero? (system* "python" "-m" "rpy2.tests" "-v")))))))
+ (propagated-inputs
+ `(("python2-six" ,python2-six)))
+ (inputs
+ `(("readline" ,readline)
+ ("icu4c" ,icu4c)
+ ("pcre" ,pcre)
+ ("r-minimal" ,r-minimal)
+ ("r-survival" ,r-survival)))
+ (native-inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://rpy.sourceforge.net/")
+ (synopsis "Python interface to the R language")
+ (description "rpy2 is a redesign and rewrite of rpy. It is providing a
+low-level interface to R from Python, a proposed high-level interface,
+including wrappers to graphical libraries, as well as R-like structures and
+functions.")
+ (license license:gpl3+)))
+
+
(define-public python-plotly ; guix candidate
; python-plotly, python-requests, python-pytz
(package