Updates to use the ghcr built container

README.md

@@ -10,15 +10,21 @@ All that's required for execution using our Docker-based setup is `Docker` with
 
 ## Building the Docker container
 
-If you are not using a pre-built container run:
+If you want to use a pre-built container run:
+
+`docker pull ghcr.io/hubmapconsortium/hra-do-processor:main`
+
+if you are not using a pre-built container run:
 
 `docker build . -t hra-do-processor`
 
 ## Running the Docker container
 
-To run the container, use the following command:
+To run using a pre-built container, use the following command:
+
+`docker run --mount type=bind,source=./digital-objects,target=/digital-objects --mount type=bind,source=./dist,target=/dist -t ghcr.io/hubmapconsortium/hra-do-processor:main help`
 
-`docker run --mount type=bind,source=./digital-objects,target=/digital-objects --mount type=bind,source=./dist,target=/dist -t hra-do-processor:latest help`
+If you are using a locally built container, replace `ghcr.io/hubmapconsortium/hra-do-processor:main` with `hra-do-processor:latest`.
 
 Replace `./digital-objects` and `./dist` with paths to your own `digital-objects` and `dist` folders if not the same.
 
@@ -36,7 +42,13 @@ You will need to install a Python 3 and Docker (or other container system suppor
 
 ## Running the DO Processor with CWL
 
-`cwl-runner hra-do-processor.cwl example-cwl-job.yaml`
+For running with a pre-built container (no git checkout required), use this command:
+
+`cwl-runner https://raw.githubusercontent.com/hubmapconsortium/hra-do-processor/main/do-processor.cwl example-cwl-job.yaml`
+
+For running with a local container, use this command:
+
+`cwl-runner do-processor.local.cwl example-cwl-job.yaml`
 
 # Running Locally
 

do-processor.cwl

@@ -0,0 +1,44 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: ghcr.io/hubmapconsortium/hra-do-processor:main
+    dockerOutputDirectory: /output
+  EnvVarRequirement:
+    envDef:
+      DO_HOME: /output/digital-objects
+      DEPLOY_HOME: /output/dist
+  InitialWorkDirRequirement:
+    listing:
+    - entryname: digital-objects
+      writable: true
+      entry: $(inputs.do_home)
+    - entryname: dist
+      writable: true
+      entry: $(inputs.deploy_home)
+
+inputs:
+  do_home:
+    type: Directory
+  deploy_home:
+    type: Directory
+  arguments:
+    type: string[]
+    inputBinding:
+      position: 1
+
+outputs:
+  do_home:
+    type: Directory
+    outputBinding:
+      glob: digital-objects
+  deploy_home:
+    type: Directory
+    outputBinding:
+      glob: dist
+  output:
+    type: stdout
+stdout: output.txt

docker-compose.yaml

@@ -1,7 +1,9 @@
 version: '3.9'
 services:
   do-processor:
-    image: hra-do-processor:latest
+    # image: ghcr.io/hubmapconsortium/hra-do-processor:main # uncomment if using the pre-built container
+    # image: hra-do-processor # uncomment if using a locally built container
+    build: . # uncomment to build locally on the fly
     volumes:
       - type: bind
         source: ./digital-objects