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-rw-r--r--gn/packages/bioinformatics.scm23
1 files changed, 16 insertions, 7 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 6774df5..94e7010 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -14,6 +14,7 @@
#:use-module (guix build-system trivial)
#:use-module (guix build-system waf)
#:use-module (gnu packages)
+ #:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
@@ -861,19 +862,19 @@ interest, and this app can provide values and figures for applicants to use.")
(license license:gpl3))))
(define-public singlecellrshiny
- (let ((commit "8061dcb477ba355de77d3e4fd3a15cf3267b56af")
- (revision "1"))
+ (let ((commit "bdca74f4819d11e8fe7b15d9ab91b853f6542f7a")
+ (revision "2"))
(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")
+ (url "https://github.com/genenetwork/singleCellRshiny")
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "1pd8a9jx6ijjggsifvq66madx31h29rah5pmz4kdzfzb4fskpqz1"))))
+ (base32 "1rxj933s9p9r7358vnp15f7ag6c0j65r4hgr8kyirfhmp1i8xdlw"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
@@ -891,13 +892,20 @@ interest, and this app can provide values and figures for applicants to use.")
(copy-recursively source targetdir)
(copy-file celltypes (string-append targetdir "/CellTypes_RGC_Master_08Dec2018.csv"))
(copy-file top1001 (string-append targetdir "/RobTop1001.csv"))
+ (substitute* (string-append targetdir "/app.R")
+ ; (("install.package.*") "")
+ ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch
+ (("library\\(DT\\)") "library(DT)\nlibrary(multtest)")
+ )
(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") celltypes)
- ;(("RobTop1001.csv") top1001)
+ (("CellTypes_RGC_Master_08Dec2018.csv") celltypes)
+ (("RobTop1001.csv") top1001)
+ ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch
+ (("dim\\(sc.object.1") "dim(sc.object")
)
(mkdir-p (string-append out "/bin"))
(call-with-output-file app
@@ -933,6 +941,7 @@ runApp(launch.browser=0, port=4208)~%\n"
(propagated-inputs
`(("r" ,r)
("r-dt" ,r-dt)
+ ("r-multtest" ,r-multtest)
("r-seurat" ,r-seurat)
("r-shiny" ,r-shiny)))
(home-page "http://rn6err.opar.io/")
@@ -940,7 +949,7 @@ runApp(launch.browser=0, port=4208)~%\n"
(description
"This is the R-Shiny programs to run some basic single cell RNA sequencing
(scRNA-seq) data analysis.")
- (license license:gpl3))))
+ (license #f))))
(define-public seqwish
(package