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-rw-r--r--gn/packages/bioinformatics.scm69
1 files changed, 69 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index f7fef26..612ce3e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -768,3 +768,72 @@ different datasets.
(description
"Display potential assembly errors in rn6.")
(license license:expat)))
+
+(define-public bxd-power-calculator-app
+ (let ((commit "7cdd73daa9a7aa79af1de04dc314c325f9706fb8")
+ (revision "1"))
+ (package
+ (name "bxd-power-calculator-app")
+ (version (git-version "0.7" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Dashbrook/BXD_power_calculator_app/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0vdfilzy78jalkh9w9xxvarnzgnlaz943crmhlds8bcrvwbmf6yh"))))
+ (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))
+ (app (string-append out "/bin/" ,name))
+ (Rbin (string-append (assoc-ref %build-inputs "r-min")
+ "/bin/Rscript"))
+ (datasets (assoc-ref %build-inputs "datasets"))
+ (source (assoc-ref %build-inputs "source")))
+ (copy-recursively source targetdir)
+ (mkdir-p (string-append out "/bin"))
+ (call-with-output-file app
+ (lambda (port)
+ (format port
+"#!~a
+library(shiny)
+setwd(\"~a\")
+runApp(launch.browser=0)~%\n"
+ Rbin targetdir)))
+ (chmod app #o555)
+ (substitute* (string-append targetdir "/server.R")
+ (("read.csv.*")
+ (string-append "read.csv(url(\"file://" datasets "\"), header = TRUE)\n")))
+ #t))))
+ (native-inputs `(("source" ,source)))
+ (propagated-inputs
+ `(("r" ,r)
+ ("r-data-table" ,r-data-table)
+ ("r-dt" ,r-dt)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-shiny" ,r-shiny)))
+ (inputs
+ `(("r-min" ,r-minimal)
+ ("datasets" ,(origin
+ (method url-fetch)
+ (uri "http://individual.utoronto.ca/D_Ashbrook/Effect_size_analysis_heritability_28th_Nov_2018_recalc.csv")
+ (sha256
+ (base32
+ "1ldr9infavd0vak8n8ry9smcnrir3xgs1bahmmx7n2csx4n6qx2x"))))))
+ (home-page "https://dashbrook1.shinyapps.io/bxd_power_calculator_app/")
+ (synopsis "Visualize probability (beta) of detecting a QTL")
+ (description
+ "The BXD power app seeks to provide a quick and easy graphical interface
+for users to calculate the theortical power to detect an effect in a two parent
+recombinant inbred population. A power calculator such as this is needed as all
+grants require a calculation of the applications power to detect the effect of
+interest, and this app can provide values and figures for applicants to use.")
+ (license license:gpl3))))