From c6ba9a5f1b75a513297e5a8dbc2b90003fe9f2a1 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 21 Sep 2017 06:22:44 +0000
Subject: Book packages

---
 gn/packages/book_evolutionary_genomics.scm | 96 ++++++++++++++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 gn/packages/book_evolutionary_genomics.scm

(limited to 'gn')

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+))))
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