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| -rw-r--r-- | gn/packages/book_evolutionary_genomics.scm | 96 |
1 files changed, 96 insertions, 0 deletions
diff --git a/gn/packages/book_evolutionary_genomics.scm b/gn/packages/book_evolutionary_genomics.scm new file mode 100644 index 0000000..eaceab7 --- /dev/null +++ b/gn/packages/book_evolutionary_genomics.scm @@ -0,0 +1,96 @@ +;; 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+)))) |