diff --git a/README.md b/README.md index 2f22b38d4..3a0161fca 100644 --- a/README.md +++ b/README.md @@ -63,6 +63,12 @@ TIBANNA_AWS_REGION # aws region (e.g. us-east-1) AWS_ACCOUNT_NUMBER # aws account number ``` +If you're using a forked repo or want to use a specific branch set the following variables accordingly and export them. If you're using default (4dn-dcic/tibanna, master), no need to set these variables. +``` +export TIBANNA_REPO_NAME=4dn-dcic/tibanna +export TIBANNA_REPO_BRANCH=master +``` + Then, set up user group and permission on AWS by using `invoke setup_tibanna_env`. ``` invoke setup_tibanna_env --buckets=,,... # add all the buckets your input/output files and log files will go to. The buckets must already exist. diff --git a/core/run_task_awsem/event.json b/core/run_task_awsem/event.json index 7c3cff7bb..b955570b7 100644 --- a/core/run_task_awsem/event.json +++ b/core/run_task_awsem/event.json @@ -34,8 +34,8 @@ "instance_type": "", "copy_to_s3": true, "launch_instance": true, - "password": "dragonfly", + "password": "", "log_bucket": "tibanna-output", - "key_name": "" + "key_name": "4dn-encode" } } diff --git a/tasks.py b/tasks.py index be203fa5b..24632414c 100644 --- a/tasks.py +++ b/tasks.py @@ -38,8 +38,8 @@ NEGATIVE = 'https://gist.github.com/j1z0/bbed486d85fb4d64825065afbfb2e98f/raw/negative.txt' AMI_ID_CWL_V1 = 'ami-31caa14e' AMI_ID_CWL_DRAFT3 = 'ami-cfb14bb5' -TIBANNA_REPO_NAME = '4dn-dcic/tibanna' -TIBANNA_REPO_BRANCH = 'master' +TIBANNA_REPO_NAME = os.environ.get('TIBANNA_REPO_NAME', '4dn-dcic/tibanna') +TIBANNA_REPO_BRANCH = os.environ.get('TIBANNA_REPO_BRANCH', 'master') def get_random_line_in_gist(url):