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-rw-r--r--gn/packages/book_evolutionary_genomics.scm96
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+;; Module that goes with the 'Evolutionary Genomics' book
+
+(define-module (gn packages genenetwork)
+ #: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 base)
+ #:use-module (gnu packages bioinformatics)
+ #:use-module (gnu packages compression)
+ ; #:use-module (gnu packages gcc)
+ ; #:use-module (gnu packages graphviz)
+ ; #:use-module (gnu packages java)
+ ; #:use-module (gnu packages linux)
+ ; #:use-module (gnu packages ldc)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages statistics)
+ #:use-module (gnu packages vim)
+ ; #:use-module (gnu packages web)
+ ; #:use-module (gnu packages xml)
+ #:use-module (gnu packages version-control)
+
+ #:use-module (gn packages bioinformatics)
+ #:use-module (gn packages javascript)
+ ; #:use-module (gn packages python)
+ ; #:use-module (gn packages statistics)
+ #:use-module (srfi srfi-1))
+
+(define-public r-gener
+ (package
+ (name "r-gener")
+ (version "2.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ ; (uri (bioconductor-uri "GeneR" version))
+ (uri "http://www.bioconductor.org/packages//2.7/bioc/src/contrib/GeneR_2.20.0.tar.gz")
+ (sha256
+ (base32
+ "1qrrq5lrm2wvx3vlas6s84spwnlaji7jaascljcr9078ww8vmjxp"))))
+ (build-system r-build-system)
+ (home-page "http://bioconductor.org/packages/GeneR")
+ (synopsis "Package manipulating nucleotidic sequences (Embl, Fasta, GenBank)")
+ (description
+ ".")
+ (license license:expat))) ; CeCILL-2.0
+
+(define-public book-evolutionary-genomics
+ (let ((md5 "93e745e9c"))
+ (package
+ (name "book-evolutionary-genomics")
+ (version "0.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri "http://files.genenetwork.org/raw_database/md5sum.txt") ; any old file
+ (file-name (string-append name "-" md5))
+ (sha256
+ (base32 "1cnkiwid4h0nnf93rm647ji9vhfzjl23arp1xj374la7mmic9jqs"))))
+ (build-system trivial-build-system)
+ (native-inputs `(("unzip" ,unzip)
+ ("source" ,source)))
+ (propagated-inputs
+ `(("python" ,python)
+ ("r" ,r)
+ ))
+ (inputs
+ `(
+ ("r-gener" ,r-gener)
+ ))
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let ((target (string-append (assoc-ref %outputs "out")
+ "/share")))
+ (write target)
+ (mkdir-p target)
+ ; (copy-recursively (assoc-ref %build-inputs "source") target)
+ #t))))
+
+ (home-page "http://github.com/pjotrp/")
+ (synopsis "Packages for Evolutionary Genomics book")
+ (description "More later...")
+ (license license:agpl3+))))