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| author | Efraim Flashner | 2020-03-03 01:31:26 -0600 |
|---|---|---|
| committer | Efraim Flashner | 2020-03-03 01:32:13 -0600 |
| commit | 91e66ebbd325ba32635d1145b0402f6ab0aaeb28 (patch) | |
| tree | 4fde7d4319b4a4741f952c9c4b9b62b7345c1f47 | |
| parent | dce1ae9dbfe7c33dcac7f64682eb9368b6480b6d (diff) | |
| download | guix-bioinformatics-91e66ebbd325ba32635d1145b0402f6ab0aaeb28.tar.gz | |
WIP: incomplete update to singlecellrshiny.
| -rw-r--r-- | gn/packages/bioinformatics.scm | 29 |
1 files changed, 25 insertions, 4 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 4cb8c7c..6774df5 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -885,15 +885,19 @@ interest, and this app can provide values and figures for applicants to use.") (app (string-append out "/bin/" ,name)) (Rbin (string-append (assoc-ref %build-inputs "r-min") "/bin/Rscript")) + (top1001 (assoc-ref %build-inputs "RobTop1001.csv")) + (celltypes (assoc-ref %build-inputs "CellTypes_RGC_Master_08Dec2018.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 "/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") "") + ;(("^rgc.*") "") + ;(("CellTypes_RGC_Master_08Dec2018.csv") celltypes) + ;(("RobTop1001.csv") top1001) ) (mkdir-p (string-append out "/bin")) (call-with-output-file app @@ -906,7 +910,24 @@ runApp(launch.browser=0, port=4208)~%\n" Rbin targetdir))) (chmod app #o555) #t)))) - (native-inputs `(("source" ,source))) + (native-inputs + `( + ("source" ,source) + ("RobTop1001.csv" + ,(origin + (method url-fetch) + (uri "https://archive.org/download/celltypesrgcmaster08dec2018/RobTop1001.csv") + (file-name "RobTop1001.csv") + (sha256 + (base32 "0pa73kc1p8417sjvvvhp9xsbh2h8g7h85pnmm16mnv4wjalhq0gn")))) + ("CellTypes_RGC_Master_08Dec2018.csv" + ,(origin + (method url-fetch) + (uri "https://archive.org/download/celltypesrgcmaster08dec2018/CellTypes_RGC_Master_08Dec2018.csv") + (file-name "CellTypes_RGC_Master_08Dec2018.csv") + (sha256 + (base32 "0y411968np1f5g21iym9xc9yj5c1jsn94rpkwkxh9pw2z43gvghn")))) + )) (inputs `(("r-min" ,r-minimal))) (propagated-inputs |