diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 36 |
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 |