* [PATCH] Add WarpedLMM.
@ 2015-06-29 14:38 Ricardo Wurmus
2015-07-01 13:33 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-06-29 14:38 UTC (permalink / raw)
To: guix-devel
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[-- Attachment #1: 0001-gnu-Add-WarpedLMM.patch --]
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From 0362c7d01134a46530f9fe01a477c28fd3ae15ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 17 Jun 2015 12:22:19 +0200
Subject: [PATCH] gnu: Add WarpedLMM.
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
---
gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c7251c4..049e1c3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1494,6 +1494,53 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
files and writing bioinformatics applications.")
(license license:bsd-3)))
+(define-public python2-warpedlmm
+ (package
+ (name "python2-warpedlmm")
+ (version "0.21")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
+ version ".zip"))
+ (sha256
+ (base32
+ "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2 ; requires Python 2.7
+ #:phases
+ (modify-phases %standard-phases
+ (add-after
+ 'install 'remove-bin-directory
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; The "bin" directory only contains wrappers for running
+ ;; the module tests. They are not needed after the
+ ;; "check" phase.
+ (delete-file-recursively
+ (string-append (assoc-ref outputs "out") "/bin"))
+ #t)))))
+ (propagated-inputs
+ `(("python-scipy" ,python2-scipy)
+ ("python-numpy" ,python2-numpy)
+ ("python-matplotlib" ,python2-matplotlib)
+ ("python-fastlmm" ,python2-fastlmm)
+ ("python-pandas" ,python2-pandas)
+ ("python-pysnptools" ,python2-pysnptools)))
+ (native-inputs
+ `(("python-setuptools" ,python2-setuptools)
+ ("python-mock" ,python2-mock)
+ ("python-nose" ,python2-nose)
+ ("unzip" ,unzip)))
+ (home-page "https://github.com/PMBio/warpedLMM")
+ (synopsis "Implementation of warped linear mixed models")
+ (description
+ "WarpedLMM is a Python implementation of the warped linear mixed model,
+which automatically learns an optimal warping function (or transformation) for
+the phenotype as it models the data.")
+ (license license:asl2.0)))
+
(define-public pbtranscript-tofu
(let ((commit "c7bbd5472"))
(package
--
2.1.0
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] Add WarpedLMM.
2015-06-29 14:38 [PATCH] Add WarpedLMM Ricardo Wurmus
@ 2015-07-01 13:33 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-07-01 13:33 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From 0362c7d01134a46530f9fe01a477c28fd3ae15ff Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 17 Jun 2015 12:22:19 +0200
> Subject: [PATCH] gnu: Add WarpedLMM.
>
> * gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
LGTM, thanks!
Ludo’.
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