aboutsummaryrefslogtreecommitdiff
path: root/gn/packages/bioinformatics.scm
diff options
context:
space:
mode:
authorEfraim Flashner2019-12-18 03:47:14 -0600
committerEfraim Flashner2019-12-18 03:47:14 -0600
commitd0866cff48b0685e302441d879648333e181b267 (patch)
tree59a252dd64f7a6a3ace0d41b21f51de92665d0e7 /gn/packages/bioinformatics.scm
parent46d8eb7a51f785a1ecd00debfedd23610257bb63 (diff)
downloadguix-bioinformatics-d0866cff48b0685e302441d879648333e181b267.tar.gz
wip: singlecellrshiny is not yet complete
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm61
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")