;; 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 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+)))