To run CellScanner, pull the image with the docker pull command and then run
docker run -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v <path_to_user_files>:/media cellscanner_user
For example, assuming you have your input files in the Testfiles folder of myexample directory:
(base) myuser@mymachine:CellScanner app$ pwd
/home/myuser/mydocs/myexample
(base) myuser@mymachine:CellScanner app$ ls
random.py Testfiles README.md
(base) myuser@mymachine:CellScanner app$ ls Testfiles
BH_mono_48h_100.fcs coculture1_48h_100.fcs control_RCM_48h_100.fcs FP_mono_48h_100.fcs RI_mono_48h_100.fcs
you may run:
docker run -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v ./Testfiles:/media hariszaf/cellscanner_user
Content type
Image
Digest
sha256:285317760…
Size
1.9 GB
Last updated
over 1 year ago
docker pull hariszaf/cell_scanner