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| -rw-r--r-- | gn/packages/bioinformatics.scm | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 4f133f8..4b8e16b 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -857,6 +857,67 @@ 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)))) +(define-public singlecellrshiny + (let ((commit "8061dcb477ba355de77d3e4fd3a15cf3267b56af") + (revision "1")) + (package + (name "singlecellrshiny") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/syousefi/singleCellRshiny.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1pd8a9jx6ijjggsifvq66madx31h29rah5pmz4kdzfzb4fskpqz1")))) + (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")) + (source (assoc-ref %build-inputs "source"))) + (copy-recursively source targetdir) + (substitute* (string-append targetdir "/global.R") + (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") + "shinyRappToyDataset_SiamakPlay.csv") + ;; Comment out the two unreferenced files for now + (("^rgc.*") "") + ;(("CellTypes_RGC_Master_08Dec2018.csv") "") + ;(("RobTop1001.csv") "") + ) + (mkdir-p (string-append out "/bin")) + (call-with-output-file app + (lambda (port) + (format port +"#!~a +library(shiny) +setwd(\"~a\") +runApp(launch.browser=0, port=4208)~%\n" + Rbin targetdir))) + (chmod app #o555) + #t)))) + (native-inputs `(("source" ,source))) + (inputs + `(("r-min" ,r-minimal))) + (propagated-inputs + `(("r" ,r) + ("r-dt" ,r-dt) + ("r-seurat" ,r-seurat) + ("r-shiny" ,r-shiny))) + (home-page "http://rn6err.opar.io/") + (synopsis "RNA sequencing data analysis") + (description + "This is the R-Shiny programs to run some basic single cell RNA sequencing +(scRNA-seq) data analysis.") + (license license:gpl3)))) + (define-public seqwish (package (name "seqwish") |