Skip to content
This repository has been archived by the owner on May 31, 2024. It is now read-only.

Commit

Permalink
docs: Incorporate README fixes from 26dc5ad
Browse files Browse the repository at this point in the history
  • Loading branch information
adamnovak committed May 3, 2022
1 parent d979cac commit c017154
Showing 1 changed file with 6 additions and 5 deletions.
11 changes: 6 additions & 5 deletions packages/engines/toil/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,21 +7,21 @@ A Toil mono-container WES server for use with Amazon Genomics CLI.
Go to this directory and run:

```bash
docker build . -f Dockerfile -t adamnovak/toil-agc
docker build . -f Dockerfile -t toil-agc
```

### Running for Testing

Having built the container, run:

```bash
docker run -ti --rm -p "127.0.0.1:8000:8000" adamnovak/toil-agc
docker run --name toil-agc-test -ti --rm -p "127.0.0.1:8000:8000" toil-agc
```

This will start the containerized server and make it available on port 8000 on the loopback interface. You can inspect the port mapping with:

```bash
docker port "$(docker ps | grep adamnovak/toil-agc | rev | cut -f1 -d' ' | rev)"
docker port toil-agc-test
```

Then you can talk to it with e.g.:
Expand All @@ -33,7 +33,7 @@ curl -vvv "http://localhost:8000/ga4gh/wes/v1/service-info"
For debugging, you can get inside the container with:

```bash
docker exec -ti "$(docker ps | grep adamnovak/toil-agc | rev | cut -f1 -d' ' | rev)" /bin/bash
docker exec -ti toil-agc-test /bin/bash
```

### Deploying
Expand All @@ -46,6 +46,7 @@ AWS_ACCOUNT=<your-account-number> # For example, 123456789012
ECR_REPO=<your-ecr-repo> # For example, yourname/toil-agc. Needs to be created in the ECR console.
aws ecr get-login-password --region ${AWS_REGION} | docker login --username AWS --password-stdin ${AWS_ACCOUNT}.dkr.ecr.${AWS_REGION}.amazonaws.com
docker build -t ${ECR_REPO} .
docker tag adamnovak/toil-agc:latest ${AWS_ACCOUNT}.dkr.ecr.${AWS_REGION}.amazonaws.com/${ECR_REPO}:latest
docker tag ${ECR_REPO}:latest ${AWS_ACCOUNT}.dkr.ecr.${AWS_REGION}.amazonaws.com/${ECR_REPO}:latest
docker push ${AWS_ACCOUNT}.dkr.ecr.${AWS_REGION}.amazonaws.com/${ECR_REPO}:latest
```

0 comments on commit c017154

Please sign in to comment.