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authorEfraim Flashner2020-03-05 08:39:11 -0600
committerEfraim Flashner2020-03-05 08:39:11 -0600
commitd3d71158cb0cd1499970a62c3800dc64ec84ecbc (patch)
tree00859c821c7f4d3a1a6e1ddd37a21dda38d78663 /gn/packages/bioinformatics.scm
parent3c3c3e830ccc4fe56f6db77e770bd533c7bdc96a (diff)
downloadguix-bioinformatics-d3d71158cb0cd1499970a62c3800dc64ec84ecbc.tar.gz
gn: singlecellrshiny is ready
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm36
1 files changed, 16 insertions, 20 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 94e7010..40a992a 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -863,7 +863,7 @@ interest, and this app can provide values and figures for applicants to use.")
(define-public singlecellrshiny
(let ((commit "bdca74f4819d11e8fe7b15d9ab91b853f6542f7a")
- (revision "2"))
+ (revision "3"))
(package
(name "singlecellrshiny")
(version (git-version "0.0.0" revision commit))
@@ -888,25 +888,18 @@ interest, and this app can provide values and figures for applicants to use.")
"/bin/Rscript"))
(top1001 (assoc-ref %build-inputs "RobTop1001.csv"))
(celltypes (assoc-ref %build-inputs "CellTypes_RGC_Master_08Dec2018.csv"))
+ (800-H1 (assoc-ref %build-inputs "800-H1-H20-RNA-Seq.csv"))
(source (assoc-ref %build-inputs "source")))
(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)")
- )
+ (("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.*") "")
+ (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") 800-H1)
(("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")
- )
+ (("dim\\(sc.object.1") "dim(sc.object"))
(mkdir-p (string-append out "/bin"))
(call-with-output-file app
(lambda (port)
@@ -918,9 +911,8 @@ runApp(launch.browser=0, port=4208)~%\n"
Rbin targetdir)))
(chmod app #o555)
#t))))
- (native-inputs
- `(
- ("source" ,source)
+ (inputs
+ `(("r-min" ,r-minimal)
("RobTop1001.csv"
,(origin
(method url-fetch)
@@ -935,21 +927,25 @@ runApp(launch.browser=0, port=4208)~%\n"
(file-name "CellTypes_RGC_Master_08Dec2018.csv")
(sha256
(base32 "0y411968np1f5g21iym9xc9yj5c1jsn94rpkwkxh9pw2z43gvghn"))))
- ))
- (inputs
- `(("r-min" ,r-minimal)))
+ ("800-H1-H20-RNA-Seq.csv"
+ ,(origin
+ (method url-fetch)
+ (uri "https://archive.org/download/celltypesrgcmaster08dec2018/800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
+ (file-name "800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
+ (sha256
+ (base32 "1b1y4lfs8drypm04i1rypbmk67rdqgs27nfh05pwnv3sja2nanam"))))))
(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/")
+ (home-page "")
(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 #f))))
+ (license license:agpl3))))
(define-public seqwish
(package