* [PATCH] Add fastlmm & pysnptools.
@ 2015-06-23 11:17 Ricardo Wurmus
2015-06-26 12:54 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-06-23 11:17 UTC (permalink / raw)
To: guix-devel
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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
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] Add fastlmm & pysnptools.
2015-06-23 11:17 [PATCH] Add fastlmm & pysnptools Ricardo Wurmus
@ 2015-06-26 12:54 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-06-26 12:54 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> 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.
LGTM.
> + (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.")
Maybe add those sentences, taken from the web page, to make it more
precise:
It can, for example, efficiently read whole PLINK *.bed/bim/fam files
or parts of those files. It can also efficiently manipulate ranges of
integers using set operators such as union, intersection, and
difference.
> 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.
OK!
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 2+ messages in thread
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2015-06-23 11:17 [PATCH] Add fastlmm & pysnptools Ricardo Wurmus
2015-06-26 12:54 ` Ludovic Courtès
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