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| -rw-r--r-- | gn/packages/book_evolutionary_genomics.scm | 126 |
1 files changed, 0 insertions, 126 deletions
diff --git a/gn/packages/book_evolutionary_genomics.scm b/gn/packages/book_evolutionary_genomics.scm deleted file mode 100644 index 56b0572..0000000 --- a/gn/packages/book_evolutionary_genomics.scm +++ /dev/null @@ -1,126 +0,0 @@ -;; 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+))) - ) |