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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 perl)
#:use-module (gnu packages python)
#:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tls)
#: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 ;; poor implementation
(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 r-soap ;; obsolete package and fails to build
(package
(name "r-soap")
(version "1.1.4")
(source
(origin
(method url-fetch)
(uri "https://sourceforge.net/projects/rsoap/files/RSOAP/1.1.4/RSOAP-1.1.4.tar.gz/download")
(sha256
(base32
"0vggycbjnjpx2c4q4wgaxfd0ig3prw31gdw9djjkbmzc3crbhj8j"))))
(propagated-inputs
`(("python" ,python)
("r" ,r)
))
(build-system r-build-system)
(home-page "https://sourceforge.net/projects/rsoap/")
(synopsis "SOAP server for R")
(description
".")
(license license:expat))) ; CeCILL-2.0
(define-public r-rserve
(package
(name "r-rserve")
(version "1.8-4")
(source
(origin
(method url-fetch)
(uri "https://github.com/s-u/Rserve/releases/download/1.8-4/Rserve_1.8-4.tar.gz")
(sha256
(base32
"1dncwiyhy1s1pimb6f2dzs3ivahah5id3chw4r10j92754bxmrn2"))))
(propagated-inputs
`(("r" ,r)))
(inputs `(("zlib" ,zlib)
("openssl" ,openssl)))
(build-system r-build-system)
(home-page "https://github.com/s-u/Rserve")
(synopsis "Fast, flexible and powerful server providing access to R from many languages and systems http://RForge.net/Rserve")
(description
"Rserve acts as a socket server (TCP/IP or local sockets) which
allows binary requests to be sent to R. Every connection has a
separate workspace and working directory. Client-side implementations
are available for popular languages such as C/C++ and Java, allowing
any application to use facilities of R without the need of linking to
R code. Rserve supports remote connection, user authentication and
file transfer. A simple R client is included in this package as
well.")
(license license:gpl2)))
(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)
("python-biopython" ,python-biopython)
("python-rserve" ,python-rserve)
("r" ,r)
("r-gener" ,r-gener)
("r-biostrings" ,r-biostrings)
("python-rpy2" ,python-rpy2)
("r-rserve" ,r-rserve)
("ruby" ,ruby)
("bioruby" ,bioruby)
("perl" ,perl)
("bioperl-minimal" ,bioperl-minimal)
("emboss" ,emboss)
))
(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+))))
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