From c017154ee13261c3f4b93954dcad6a9ff7a41b37 Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Tue, 3 May 2022 08:55:26 -0700 Subject: [PATCH] docs: Incorporate README fixes from 26dc5add --- packages/engines/toil/README.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/packages/engines/toil/README.md b/packages/engines/toil/README.md index 5295a231..cf102dfa 100644 --- a/packages/engines/toil/README.md +++ b/packages/engines/toil/README.md @@ -7,7 +7,7 @@ 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 @@ -15,13 +15,13 @@ docker build . -f Dockerfile -t adamnovak/toil-agc 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 "$(docker ps | grep adamnovak/toil-agc | rev | cut -f1 -d' ' | rev)" +docker port toil-agc-test ``` Then you can talk to it with e.g.: @@ -33,7 +33,7 @@ curl -vvv "http://localhost:8000/ga4gh/wes/v1/service-info" For debugging, you can get inside the container with: ```bash -docker exec -ti "$(docker ps | grep adamnovak/toil-agc | rev | cut -f1 -d' ' | rev)" /bin/bash +docker exec -ti toil-agc-test /bin/bash ``` ### Deploying @@ -46,6 +46,7 @@ AWS_ACCOUNT= # For example, 123456789012 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 ``` +