Launch CaDrA’s Shiny Dashboard with Docker

Source: vignettes/docker.Rmd

Software requirements

  • Git version >= 2.21
  • Docker version >= 20.10

Don’t have Git installed, see Git Guides

Don’t have Docker installed, see Docker Engine

Build Docker image of CaDrA.shiny

(1) Clone this repository 

git clone https://github.com/montilab/CaDrA.shiny.git

(2) Navigate to CaDrA.shiny folder where Dockerfile is stored and build its Docker image. 

docker build -t cadra.shiny:latest .

-t: add a tag to an image such as the version of the application, e.g. cadra.shiny:1.0.0 or cadra.shiny:latest.

(3) After the build is completed, check if the image is built successfully 

docker images

REPOSITORY        TAG        IMAGE ID        CREATED        SIZE
cadra.shiny       latest     2c22887402d3    2 hours ago    2.56GB

Run CaDrA.shiny container with its built image

(1) Mount appropriate data inputs and code base to the container 

docker run \
-v /path/to/CaDrA.shiny:/CaDrA.shiny \
-v /path/to/CaDrA.shiny/inst/extdata:/CaDrA.shiny/inst/extdata \
-p 4567:3838 --name cadra.shiny \
-d cadra.shiny:latest

-v: mount code base or data files from host directory to container directory [host_div]:[container_dir].
-p: map host port to container port [host_port]:[container_port]
--name: give an identity to the container
-d: run container in detached mode

For more information about the Docker syntax, see Docker run reference

NOTE:

  • Change /path/to/CaDrA.shiny to your local CaDrA.shiny directory. This directory contains the code base of CaDrA.shiny needed to build its Shiny dashboard.
  • Change /path/to/CaDrA.shiny/inst/extdata to your local CaDrA.shiny/inst/extdata directory. In this directory, you can place any external data files (e.g. feature sets, gene expression sets, input scores, etc.) in which you would like to populate the CaDrA.shiny dashboard with. However, a datalist.csv or datalist.RDS must be provided at the root of the directory including names and paths of where to import these data files into CaDrA.shiny dashboard.

    The datalist.csv or datalist.RDS must contain the following fields:
Fields Description Values
feature_set_name Alias name for a feature set Required.
e.g. TCGA_ACC_2016_01_28_GISTIC_MUT_SIG
feature_set_path Absolute path to a feature set file. File format: csv or rds. Required.
e.g. /CaDrA.shiny/inst/extdata/feature_set/TCGA_ACC_2016_01_28_GISTIC_MUT_SIG.rds
input_score_name Alias name for an input score Optional.
input_score_path Absolute path to an input score file. File format: csv or rds. Optional.
gene_expression_name Alias name for a gene expression set Optional.
gene_expression_path Absolute path to a gene expression set file. File format: csv or rds. Optional.

An example of datalist.csv:

feature_set_name feature_set_path input_score_name input_score_path gene_expression_name gene_expression_path
CCLE SCNAs and Mutations /CaDrA.shiny/inst/extdata/CCLE_MUT_SCNA.rds B-catenin Activity in CCLE /CaDrA.shiny/inst/extdata/CTNBB1_reporter.rds
TCGA BrCa SCNAs and Mutations /CaDrA.shiny/inst/extdata/BRCA_GISTIC_MUT_SIG.rds YAP/TAZ Activity in TCGA BrCa /CaDrA.shiny/inst/extdata/TAZYAP_BRCA_ACTIVITY.rds
Simulated Feature Set /CaDrA.shiny/inst/extdata/sim_FS.rds Simulated Input Score /CaDrA.shiny/inst/extdata/sim_Scores.rds

IMPORTANT NOTE: Since Docker does not have direct access to the host machine, we must list each data file in its absolute path as referenced to its mounted directory inside the container (e.g. /CaDrA.shiny/inst/extdata) not the host directory.

(2) Check if the container is built successfully 

docker ps


CONTAINER ID   IMAGE               COMMAND                    CREATED        STATUS        PORTS                    NAMES
b37b6b19c4e8   cadra.shiny:latest  "/bin/bash -c /user/..."   5 hours ago    Up 5 hours    0.0.0.0:4567->3838/tcp   cadra.shiny

Based on the output above, the cadra.shiny dashboard is published on port 4567 on the host machine, and 3838 is the port of where the cadra.shiny is published inside the Docker container. Noted that all requests that are made to the host machine will be automatically redirected to the Docker container where the Shiny app is launched and deployed.

Access CaDrA.shiny dashboard on your localhost

Using your preferred web browser, type in http://localhost:4567 and see if CaDrA.shiny dashboard is indeed hosted there.



Any questions or issues? Please report them on our github issues.