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-;; Module that goes with the 'Evolutionary Genomics' book
-
-(define-module (gn packages book_evolutionary_genomics)
- #: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 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 cran)
- #:use-module (gnu packages libffi)
- #: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 version-control)
-
- #:use-module (gn packages bioinformatics)
- #:use-module (gn packages javascript)
- #:use-module (gn packages python)
- #: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 book-evolutionary-genomics
- (let ((commit "53a7aefefcedd52b94b38195f8daae94c07d89db"))
- (package
- (name "book-evolutionary-genomics")
- (version (string-append "0.2.1" "-" (string-take commit 7) ))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pjotrp/Cross-language-interfacing.git")
- (commit commit)))
- (file-name (string-append name "-" version))
- (sha256
- (base32
- "00amdba2vjwxjhrikaym2xacszhcmiqyc6iknlhdbi86ccmf5qbp"))))
- (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-cffi" ,python-cffi)
- ("python-rpy2" ,python-rpy2)
- ("r-rserve" ,r-rserve)
- ("ruby" ,ruby)
- ("ruby-ffi" ,ruby-ffi)
- ("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/book-evolutionary-genomics")))
- (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+)))
- )