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;; Bioinformatics module
(define-module (gn packages bioinformatics)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
#:use-module (guix build-system ruby)
#:use-module (guix build-system r)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages file)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages zip)
#:use-module (gnu packages bootstrap)
#:use-module (srfi srfi-1))
(define-public my-deploy
(package
(name "my-deploy")
(version "0.0.1")
(source #f)
(build-system trivial-build-system)
(arguments
`(#:guile ,%bootstrap-guile
#:modules ((guix build utils))
#:builder
(let* ((out (assoc-ref %outputs "out"))
(bash (assoc-ref %build-inputs "bash"))
(foo (string-append out "/foo")))
(begin
(use-modules (guix build utils))
(mkdir out)
(call-with-output-file foo
(lambda (p)
(format p
"#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%"
bash)))
(chmod foo #o777)
;; wrap-program uses `which' to find bash for the wrapper
;; shebang, but it can't know about the bootstrap bash in
;; the store, since it's not named "bash". Help it out a
;; bit by providing a symlink it this package's output.
(symlink bash (string-append out "/bash"))
(setenv "PATH" out)
(wrap-program foo `("GUIX_FOO" prefix ("hello")))
(wrap-program foo `("GUIX_BAR" prefix ("world")))
#t))))
(inputs `(("bash" ,(search-bootstrap-binary "bash"
(%current-system)))))
(home-page #f)
(synopsis #f)
(description #f)
(license #f)))
(define-public r-wgcna
(package
(name "r-wgcna")
(version "1.48")
(source
(origin
(method url-fetch)
(uri (cran-uri "WGCNA" version))
(sha256
(base32
"18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn"))))
(properties `((upstream-name . "WGCNA")))
(build-system r-build-system)
;; (propagated-inputs
;; `( ;; ("r-annotationdbi" ,r-annotationdbi)
;; ("r-doparallel" ,r-doparallel)
;; ("r-dynamictreecut" ,r-dynamictreecut)
;; ("r-fastcluster" ,r-fastcluster)
;; ("r-foreach" ,r-foreach)
;; ("r-go.db" ,r-go.db)
;; ("r-grdevices" ,r-grdevices)
;; ("r-hmisc" ,r-hmisc)
;; ("r-impute" ,r-impute)
;; ("r-matrixstats" ,r-matrixstats)
;; ("r-parallel" ,r-parallel)
;; ("r-preprocesscore" ,r-preprocesscore)
;; ("r-splines" ,r-splines)
;; ("r-stats" ,r-stats)
;; ("r-survival" ,r-survival)
;; ("r-utils" ,r-utils)))
(home-page
"http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
(synopsis
"Weighted Correlation Network Analysis")
(description
"Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.")
(license license:gpl2+)))
(define-public genenetwork2
(let ((commit "9e9475053"))
(package
(name "genenetwork2")
(version (string-append "2.0." commit))
(source (origin
(method git-fetch)
(uri (git-reference
;; (url "https://github.com/genenetwork/genenetwork2.git")
(url "https://github.com/pjotrp/genenetwork2.git")
(commit commit)))
(sha256
(base32
"1rzm0m596g2lh8vszfla2dz52frdzfhp0az7mrx2axmfqad90ywl"))))
(inputs `(("nginx" ,nginx)
("python-setuptools" ,python2-setuptools)
("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
("python-pandas" ,python2-pandas)
("python" ,python-2) ;; probably superfluous
("plink" ,plink) ;; probably superfluous
("r-qtl" ,r-qtl)
))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:tests? #f)) ; no 'setup.py test'
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")
(description "Genenetwork installation sumo.")
(license license:agpl3+))))
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