[PATCH] Add fastlmm & pysnptools.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

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From b88c44394c1a6e2e9a5932ac2a3a9b431408c742 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 12 Jun 2015 15:46:40 +0200
Subject: [PATCH 1/2] gnu: Add python2-pysnptools.

* gnu/packages/python.scm (python2-pysnptools): New variable.
---
 gnu/packages/python.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index d503c78..7958a5f 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2598,6 +2598,36 @@ toolkits.")
                                        (package-propagated-inputs
                                         matplotlib))))))))
 
+(define-public python2-pysnptools
+  (package
+    (name "python2-pysnptools")
+    (version "0.2.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/p/pysnptools"
+             "/pysnptools-" version ".zip"))
+       (sha256
+        (base32
+         "1rzf5qvwfvd2pp84b14pb2gdvxdk5avnj7rb41ac8gndpkr9g6ib"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2)) ; only Python 2.7 is supported
+    (propagated-inputs
+     `(("python2-numpy" ,python2-numpy)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-pandas" ,python2-pandas)
+       ("python2-cython" ,python2-cython)))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("python2-setuptools" ,python2-setuptools)))
+    (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/")
+    (synopsis "Library for reading and manipulating genetic data")
+    (description
+     "PySnpTools is a library for reading and manipulating genetic data.")
+    (license asl2.0)))
+
 (define-public python-scipy
   (package
     (name "python-scipy")
-- 
2.1.0


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From add86a77f8371e9392f696bc0608a64a898803f8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 12 Jun 2015 15:47:18 +0200
Subject: [PATCH 2/2] gnu: Add python2-fastlmm.

* gnu/packages/python.scm (python2-fastlmm): New variable.
---
 gnu/packages/python.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7958a5f..9876a3f 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2326,6 +2326,42 @@ capabilities.")
 (define python2-numpy-bootstrap
   (package-with-python2 python-numpy-bootstrap))
 
+(define-public python2-fastlmm
+  (package
+    (name "python2-fastlmm")
+    (version "0.2.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/f/fastlmm"
+             "/fastlmm-" version ".zip"))
+       (sha256
+        (base32
+         "023sydkrc3yxad2bycar02jfswwlh4199kafzhf2bssyx2c3xa0l"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2)) ; only Python 2.7 is supported
+    (propagated-inputs
+     `(("python2-numpy" ,python2-numpy)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-matplotlib" ,python2-matplotlib)
+       ("python2-pandas" ,python2-pandas)
+       ("python2-scikit-learn" ,python2-scikit-learn)
+       ("python2-cython" ,python2-cython)
+       ("python2-pysnptools" ,python2-pysnptools)))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("python2-mock" ,python2-mock)
+       ("python2-setuptools" ,python2-setuptools)))
+    (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
+    (synopsis "Perform genome-wide association studies on large data sets")
+    (description
+     "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
+Models, is a program for performing both single-SNP and SNP-set genome-wide
+association studies (GWAS) on extremely large data sets.")
+    (license asl2.0)))
+
 (define-public python-numpy
   (package (inherit python-numpy-bootstrap)
     (name "python-numpy")
-- 
2.1.0