diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 69 |
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)))) |