From 0a1882996472282dcf60f6a294a4f934d40d5bad Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Wed, 25 Oct 2017 10:17:38 +0000
Subject: Updated GEMMA git Added python-rpy2 since it got dropped from main

---
 gn/packages/gemma.scm  |  8 ++++----
 gn/packages/python.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+), 4 deletions(-)

(limited to 'gn/packages')

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
-- 
cgit v1.2.3