tthyer

#! /bin/bash

# pass tags as arguments to script
# if no arguments, nothing will be removed
# for example to remove all tags run ./remove-tags.sh $(git tag)
tags=( "$@" ) 
for i in ${tags[@]}
do
  git push --delete origin $i
  git tag -d $i

tthyer

apiVersion: batch/v1
kind: Job
metadata:
  # It is good practice to include your username in your job name.
  # Also specify it in TOIL_KUBERNETES_OWNER
  name: tthyer-toil-rna-seq-test

spec:
  # Do not try and rerun the leader job if it fails
  backoffLimit: 0

tthyer

# show that dockerhub is decrementing your allowed pulls when you re-request a "latest" image
sudo yum install jq
export TOKEN=$(curl "https://auth.docker.io/token?service=registry.docker.io&scope=repository:ratelimitpreview/test:pull" | jq -j '.token'); echo $TOKEN
while true; do
  echo $(curl --head -H "Authorization: Bearer $TOKEN" https://registry-1.docker.io/v2/ratelimitpreview/test/manifests/latest 2>&1 | grep RateLimit-Remaining)
  docker pull alpine:latest
  sleep 3
done

tthyer

{
    "write_to_cache": false,
    "read_from_cache": false,
    "default_runtime_attributes": {
      "maxRetries": 2
    }
}

tthyer

aws --profile sandbox-admin cloudformation create-stack \
  --stack-name tthyer-cromwell-test \
  --template-body file://src/templates/cromwell/cromwell-resources.template.yaml \
  --capabilities CAPABILITY_IAM \
  --parameters \
    ParameterKey=Namespace,ParameterValue=tthyer-cromwell-test \
    ParameterKey=GWFCoreNamespace,ParameterValue=tthyer-cromwell-test-gwfcore \
    ParameterKey=VpcId,ParameterValue=vpc-0e9b80dc470a797d5 \
    ParameterKey=ServerSubnetID,ParameterValue=subnet-025c297e427e44daf \
    ParameterKey=DBSubnetIDs,ParameterValue=\"subnet-025c297e427e44daf,subnet-0b8a92e98f330a943\" \

tthyer

#! /usr/bin/bash

set -ex

amazon-linux-extras install python3.8 --yes

python3.8 -m pip install --upgrade pip

pip install synapseclient # boto3 should already be installed but if not install that here

tthyer

#! /bin/bash
# Script to execute a SQL query through awscli

set -ex

CLUSTER_ARN='arn:aws:rds:us-east-1:035458030717:cluster:tower'
SECRET_ARN=$(aws secretsmanager describe-secret \
  --secret-id nextflow-aurora-mysql-MasterSecret | jq -r .ARN)

QUERY="${1}"

tthyer

tthyer

aws glue get-table --database-name $DBNAME --name TABLENAME | jq -r '.Table.StorageDescriptor.Columns[].Name'

tthyer

-- check kds_landing stats
SELECT * FROM metrics.kds_landing_stats ORDER BY stats_update_time DESC;

-- get row counts for each date in metrics.metrics
SELECT TRUNC(interval_start) as interval_date, COUNT(*) as row_count
       FROM metrics.metrics
GROUP BY interval_date
ORDER BY interval_date;

-- get stats for refresh duration for each materialized view