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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-06-17 12:22:19 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-07-02 11:16:46 +0200 |
| commit | c61fe02cc03178c2d6947de7e49c72f2abb73b7c (patch) | |
| tree | d0fee3157ac2cd393261126153e555341c97e389 /gnu | |
| parent | f4f4ced8dccba6bc0b7c5d5e4c90cdb6488d1faf (diff) | |
| download | patches-c61fe02cc03178c2d6947de7e49c72f2abb73b7c.tar patches-c61fe02cc03178c2d6947de7e49c72f2abb73b7c.tar.gz | |
gnu: Add WarpedLMM.
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c7251c4c20..049e1c3308 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 |