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authorEfraim Flashner2020-03-03 01:31:26 -0600
committerEfraim Flashner2020-03-03 01:32:13 -0600
commit91e66ebbd325ba32635d1145b0402f6ab0aaeb28 (patch)
tree4fde7d4319b4a4741f952c9c4b9b62b7345c1f47 /gn
parentdce1ae9dbfe7c33dcac7f64682eb9368b6480b6d (diff)
downloadguix-bioinformatics-91e66ebbd325ba32635d1145b0402f6ab0aaeb28.tar.gz
WIP: incomplete update to singlecellrshiny.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm29
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