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authorEfraim Flashner2019-09-26 08:42:47 -0500
committerEfraim Flashner2019-09-26 08:42:47 -0500
commitd7bffaf6b1cb7a952b510d37caf2e0ff132b95ea (patch)
treece7eff8be0da920b99f03339073e4e75ff91d07f
parentaa268c3d47e1abf6da78bf576be813d3977c6e72 (diff)
downloadguix-bioinformatics-d7bffaf6b1cb7a952b510d37caf2e0ff132b95ea.tar.gz
gn: Add rn6-assembly-error-app.
* gn/packages/bioinformatics.scm (rn6-assembly-error-app): New variable.
-rw-r--r--gn/packages/bioinformatics.scm56
1 files changed, 54 insertions, 2 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 726eed2..373ce2f 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -10,14 +10,18 @@
#:use-module (guix build-system ant)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
- #:use-module (guix build-system waf)
#:use-module (guix build-system python)
+ #:use-module (guix build-system trivial)
+ #:use-module (guix build-system waf)
#:use-module (gnu packages)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
- #:use-module (gnu packages compression)
#:use-module (gnu packages check)
+ #:use-module (gnu packages compression)
+ #:use-module (gnu packages cran)
+ #:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
+ #:use-module (gnu packages imagemagick)
#:use-module (gnu packages maths)
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
@@ -716,3 +720,51 @@ different datasets.
@item To compute 'genetic risk predictor' scores.
@end enumerate")
(license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt")))))
+
+(define-public rn6-assembly-error-app
+ (package
+ (name "rn6-assembly-error-app")
+ (version "0.11")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/chen42/rn6_assembly_error_app.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0ck3ndii24k4whlmiiv46120wwq5hnndwff83iaiavg703f337y1"))))
+ (build-system trivial-build-system)
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let* ((out (assoc-ref %outputs "out"))
+ (targetdir (string-append out "/share/" ,name))
+ (ggplot2 (assoc-ref %build-inputs "r-ggplot2"))
+ (shiny (assoc-ref %build-inputs "r-shiny"))
+ (convert (string-append (assoc-ref %build-inputs "imagemagick")
+ "/bin/convert"))
+ (source (assoc-ref %build-inputs "source")))
+ ;; Copied from https://stackoverflow.com/questions/2698269/how-do-you-change-library-location-in-r
+ (copy-recursively source targetdir)
+ (substitute* (string-append targetdir "/server.r")
+ (("library\\(\"shiny\"" prefix)
+ (string-append prefix ",lib.loc=" shiny "/site-library\""))
+ (("library\\(\"ggplot2\"" prefix)
+ (string-append prefix ",lib.loc=" ggplot2 "/site-library\""))
+ (("convert") convert)
+ )
+ #t))))
+ (native-inputs `(("source" ,source)))
+ (inputs
+ `(("imagemagick" ,imagemagick)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-shiny" ,r-shiny)))
+ (propagated-inputs
+ `(("freetype" ,freetype)))
+ (home-page "http://rn6err.opar.io/") ; or similar
+ (synopsis "Display potential assembly errors in rn6")
+ (description
+ "Display potential assembly errors in rn6.")
+ (license #f)))