From b4887cef698a44fd79a55a0f1f0a16cb8d7e7c01 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 30 Apr 2021 05:39:08 -0400
Subject: Remove book module which is obsolete

---
 gn/packages/book_evolutionary_genomics.scm | 126 -----------------------------
 1 file changed, 126 deletions(-)
 delete mode 100644 gn/packages/book_evolutionary_genomics.scm

(limited to 'gn/packages')

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+)))
-  )
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