README.md

deepmaps-api

The package is the R API server for DeepMAPS website.

Installation

R package

library(devtools)
install_github("Wang-Cankun/iris3api@master")

Docker build

We split the package to 2 containers, as it can speed up the build and deployment time (40 min -> 5 min).

To build the docker image, enter project root directory first.

Base image

This base image contains all necessary for the package. Including plumber, Seurat, Signac, tidyverse, BioConductor suite (GenomicRanges, SingleCellExperiment, etc.)

# Build
docker build -f base.Dockerfile -t wangcankun100/deepmaps-api-base .

# Test what packages are installed
docker run wangcankun100/deepmaps-api-base

Client image

This client image builds upon the deepmaps-api-base image. It will only install the R package itself.

# Build
docker build --no-cache -f R-client.Dockerfile -t wangcankun100/deepmaps-r-client .
docker push wangcankun100/deepmaps-r-client

# Deploy
docker pull wangcankun100/deepmaps-r-client
docker run -d -v /var/www/nodejs/data/:/data --name deepmaps-r-client -p 8000:8000 wangcankun100/deepmaps-r-client
docker logs deepmaps-r-client
docker restart deepmaps-r-client

# Run
docker run --rm -p 8000:8000 wangcankun100/deepmaps-r-client
docker run -v /var/www/nodejs/data/:/data -p 8000:8000 wangcankun100/deepmaps-r-client