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| author | Efraim Flashner | 2019-09-26 08:42:47 -0500 |
|---|---|---|
| committer | Efraim Flashner | 2019-09-26 08:42:47 -0500 |
| commit | d7bffaf6b1cb7a952b510d37caf2e0ff132b95ea (patch) | |
| tree | ce7eff8be0da920b99f03339073e4e75ff91d07f /gn/packages/bioinformatics.scm | |
| parent | aa268c3d47e1abf6da78bf576be813d3977c6e72 (diff) | |
| download | guix-bioinformatics-d7bffaf6b1cb7a952b510d37caf2e0ff132b95ea.tar.gz | |
gn: Add rn6-assembly-error-app.
* gn/packages/bioinformatics.scm (rn6-assembly-error-app): New variable.
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 56 |
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))) |