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Fixed several issues I ran into #15

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Fixed several issues I ran into #15

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70b3701
Changed isaac dockerfile base image, as isaac build was failing with …
Aug 9, 2019
1dd66fa
Corrected the template filepaths. Were pointing
Sep 20, 2019
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8 changes: 4 additions & 4 deletions pipeline/nested_templates/batch_jobs_template_cfn.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ Resources:
ReferenceS3Path: "s3://aws-batch-genomics-shared/secondary-analysis/reference/isaac/"
WorkingDir: "/scratch"
ContainerProperties:
Image: !Sub "${AWS::AccountId}.dkr.ecr.us-east-1.amazonaws.com/isaac"
Image: !Sub "${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/isaac"
Vcpus: 32
Memory: 80000
JobRoleArn:
Expand Down Expand Up @@ -69,7 +69,7 @@ Resources:
VCFS3Path: !Sub "s3://${JobResultsBucket}/${DefaultSampleName}/vcf"
WorkingDir: "/scratch"
ContainerProperties:
Image: !Sub "${AWS::AccountId}.dkr.ecr.us-east-1.amazonaws.com/strelka"
Image: !Sub "${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/strelka"
Vcpus: 32
Memory: 32000
JobRoleArn:
Expand Down Expand Up @@ -109,7 +109,7 @@ Resources:
CommandArgs: " -t hg38 "
WorkingDir: "/scratch"
ContainerProperties:
Image: !Sub "${AWS::AccountId}.dkr.ecr.us-east-1.amazonaws.com/snpeff"
Image: !Sub "${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/snpeff"
Vcpus: 4
Memory: 10000
JobRoleArn:
Expand Down Expand Up @@ -145,7 +145,7 @@ Resources:
BAMStatsS3Path: !Sub "s3://${JobResultsBucket}/${DefaultSampleName}/bam/sorted.bam.stats"
WorkingDir: "/scratch"
ContainerProperties:
Image: !Sub "${AWS::AccountId}.dkr.ecr.us-east-1.amazonaws.com/samtools-stats"
Image: !Sub "${AWS::AccountId}.dkr.ecr.${AWS::Region}.amazonaws.com/samtools-stats"
Vcpus: 4
Memory: 40000
JobRoleArn:
Expand Down
2 changes: 1 addition & 1 deletion tools/isaac/docker/Dockerfile
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@@ -1,4 +1,4 @@
FROM python:2.7
FROM python:2.7-stretch

ARG VERSION="03.17.03.01"

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10 changes: 5 additions & 5 deletions tools/template_cfn.yml
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Expand Up @@ -157,7 +157,7 @@ Resources:
"Volume": {
"type": "String",
"description": "Volume to mount.",
"default": "/dev/nvme1n1"
"default": "/dev/sdb"
},
"TargetAmiName": {
"type": "String",
Expand Down Expand Up @@ -281,11 +281,11 @@ Resources:
"set -e",
"yum -y update",
"yum -y install parted",
"parted /dev/nvme1n1 mklabel gpt -s",
"parted /dev/nvme1n1 mkpart primary 0% 100% -s",
"mkfs -t ext4 -F /dev/nvme1n1",
"parted {{Volume}} mklabel gpt -s",
"parted {{Volume}} mkpart primary 0% 100% -s",
"mkfs -t ext4 -F {{Volume}}",
"mkdir /docker_scratch",
"echo -e '/dev/nvme1n1\t/docker_scratch\text4\tdefaults\t0\t0' | sudo tee -a /etc/fstab",
"echo -e '{{Volume}}\t/docker_scratch\text4\tdefaults\t0\t0' | sudo tee -a /etc/fstab",
"mount -a"
]
}
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4 changes: 2 additions & 2 deletions update.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ cd ..

# Update Zone Stack

aws cloudformation update-stack --stack-name batch-genomics-zone --template-body file://zone_template_cfn.yml --capabilities CAPABILITY_NAMED_IAM --output text;aws cloudformation wait stack-create-complete --stack-name batch-genomics-zone
aws cloudformation update-stack --stack-name batch-genomics-zone --template-body file://template_cfn.yml --capabilities CAPABILITY_NAMED_IAM --output text;aws cloudformation wait stack-create-complete --stack-name batch-genomics-zone

cd tools

Expand All @@ -26,6 +26,6 @@ cd pipeline

IMAGE_ID=$(aws cloudformation describe-stacks --stack-name batch-genomics-pipeline --query 'Stacks[].Outputs[?OutputKey==`ImageId`].OutputValue' --output text)

aws cloudformation update-stack --stack-name batch-genomics-pipeline --template-body file://pipeline/template_cfn.yml --capabilities CAPABILITY_NAMED_IAM --output text --parameters ParameterKey=TemplatesBucket,ParameterValue=${TEMPLATES_BUCKET} ParameterKey=ImageId,ParameterValue=${IMAGE_ID};aws cloudformation wait stack-update-complete --stack-name batch-genomics-pipeline
aws cloudformation update-stack --stack-name batch-genomics-pipeline --template-body file://template_cfn.yml --capabilities CAPABILITY_NAMED_IAM --output text --parameters ParameterKey=TemplatesBucket,ParameterValue=${TEMPLATES_BUCKET} ParameterKey=ImageId,ParameterValue=${IMAGE_ID};aws cloudformation wait stack-update-complete --stack-name batch-genomics-pipeline

cd ..