OpenCPU in Docker

Build

Default

docker build -t cannin/opencpu:opencpu-2.0 .
docker build -t cannin/opencpu:enrichmentmap -f Dockerfile_enrichmentmap .

Custom Install

docker build -t cannin/opencpu:enrichmentmap -f Dockerfile_enrichmentmap .
docker pull cannin/opencpu:enrichmentmap

Run

Default

docker rm -f oc; docker run --name oc -t -p 80:80 -p 8004:8004 cannin/opencpu
docker rm -f oc; docker run --name oc -it -p 80:80 -p 8004:8004 cannin/opencpu bash
docker exec -it oc bash

Custom Container

# SKIP: docker rm -f oc; docker run --name oc -t -p 80:80 -p 8004:8004 cannin/opencpu:enrichmentmap
docker rm -f oc; docker run --name oc -it -p 80:80 -p 8004:8004 cannin/opencpu:enrichmentmap apache2ctl -D FOREGROUND
docker rm -f oc; docker run --name oc -it -p 80:80 -p 8004:8004 cannin/opencpu:enrichmentmap bash
docker exec -it oc bash

Call OpenCPU

curl http://localhost/ocpu/library/stats/R/rnorm/json -d "n=10&mean=5"

Access output and files

Public

curl http://public.opencpu.org/ocpu/library/stats/R/rnorm -d "n=10&mean=5"
curl http://public.opencpu.org/ocpu/tmp/x09e692cd2c/R/.val
curl http://public.opencpu.org/ocpu/tmp/x09e692cd2c/files/DESCRIPTION

Local/Custom Package

Generate a table with a set number of rows/columns

curl http://localhost/ocpu/library/enrichmentmap/R/getMatrix/json -d "n=100&r=10&c=10"

Call command that creates JSON file

curl http://localhost/ocpu/library/enrichmentmap/R/getJson -d "saveFile=TRUE"

Access JSON file

• NOTE: The ID "x06ee947c11" will change. The output from getJson will specify the ID.

curl http://localhost/ocpu/tmp/x06ee947c11/R/.val/print
curl http://localhost/ocpu/tmp/x06ee947c11/files/example.json

Access JSON output from function

The output from x can be parsed using JSON.parse()

• NOTE: Without parameters the function is returned

x = curl http://localhost/ocpu/library/enrichmentmap/R/getJsonStr/json -d "p=0"
JSON.parse(x)

Run getEnrichmentMap

Test

• Test at this URL: http://127.0.0.1/ocpu
• URL: ../library/enrichmentmap/R/getEnrichmentMap/json
• Parameter: genes: ["BRAF", "MDM2", "TP53"]
• Request type: POST