def make_input(bucket_name, key, uuid):
data = {"parameters": {},
"app_name": "fastqc-0-11-4-1",
"workflow_uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9",
"input_files": [
{"workflow_argument_name": "input_fastq",
"bucket_name": bucket_name,
"uuid": str(uuid),
"object_key": str(key),
}
],
"output_bucket": "elasticbeanstalk-encoded-4dn-wfoutput-files",
}
data.update(_tibanna_settings({'run_id': str(key),
'run_type': 'fastqc'}))
return data
def _make_input(env,
bucket,
workflow,
object_key,
uuid,
run_name,
dependency=None):
output_bucket = "elasticbeanstalk-%s-wfoutput" % env
workflow_uuid = _workflows[workflow]['uuid']
workflow_arg_name = _workflows[workflow]['arg_name']
data = {
"parameters": {},
"app_name":
workflow,
"workflow_uuid":
workflow_uuid,
"input_files": [{
"workflow_argument_name": workflow_arg_name,
"bucket_name": bucket,
"uuid": uuid,
"object_key": object_key,
}],
"output_bucket":
output_bucket,
"config": {
"ebs_type": "io1",
"json_bucket": "4dn-aws-pipeline-run-json",
"ebs_iops": 500,
"shutdown_min": 0,
"password": "******",
"log_bucket": "tibanna-output",
"key_name": "4dn-encode"
}
}
if dependency:
data["dependency"] = {"exec_arn": dependency}
data.update(
_tibanna_settings({
'run_id': str(object_key),
'run_name': run_name,
'run_type': workflow,
'env': env,
}))
return data
def make_input(bucket_name, key, uuid):
data = {
"parameters": {},
"app_name":
"fastqc-0-11-4-1",
"workflow_uuid":
"2324ad76-ff37-4157-8bcc-3ce72b7dace9",
"input_files": [{
"workflow_argument_name": "input_fastq",
"bucket_name": bucket_name,
"uuid": str(uuid),
"object_key": str(key),
}],
"output_bucket":
"elasticbeanstalk-encoded-4dn-wfoutput-files",
}
data.update(_tibanna_settings({'run_id': str(key), 'run_type': 'fastqc'}))
return data
def make_input(env, workflow, accession, uuid):
bucket = "elasticbeanstalk-%s-files" % env
output_bucket = "elasticbeanstalk-%s-wfoutput" % env
workflow_uuid = _workflows[workflow]['uuid']
workflow_arg_name = _workflows[workflow]['arg_name']
data = {
"parameters": {},
"app_name":
workflow,
"workflow_uuid":
workflow_uuid,
"input_files": [{
"workflow_argument_name": workflow_arg_name,
"bucket_name": bucket,
"uuid": uuid,
"object_key": accession,
}],
"output_bucket":
output_bucket,
"config": {
"ebs_type": "io1",
"json_bucket": "4dn-aws-pipeline-run-json",
"ebs_iops": 500,
"shutdown_min": 30,
"s3_access_arn":
"arn:aws:iam::643366669028:instance-profile/S3_access",
"ami_id": "ami-7ff26968",
"copy_to_s3": True,
"script_url":
"https://raw.githubusercontent.com/4dn-dcic/tibanna/master/awsf/",
"launch_instance": True,
"password": "******",
"log_bucket": "tibanna-output",
"key_name": "4dn-encode"
},
}
data.update(
_tibanna_settings({
'run_id': str(accession),
'run_type': workflow,
'env': env,
}))
return data
def make_input(env, workflow, object_key, uuid):
bucket = "elasticbeanstalk-%s-files" % env
output_bucket = "elasticbeanstalk-%s-wfoutput" % env
workflow_uuid = _workflows[workflow]['uuid']
workflow_arg_name = _workflows[workflow]['arg_name']
data = {
"parameters": {},
"app_name":
workflow,
"workflow_uuid":
workflow_uuid,
"input_files": [{
"workflow_argument_name": workflow_arg_name,
"bucket_name": bucket,
"uuid": uuid,
"object_key": object_key,
}],
"output_bucket":
output_bucket,
"config": {
"ebs_type": "io1",
"json_bucket": "4dn-aws-pipeline-run-json",
"ebs_iops": 500,
"shutdown_min": 30,
"ami_id": "ami-cfb14bb5",
"copy_to_s3": True,
"script_url":
"https://raw.githubusercontent.com/4dn-dcic/tibanna/master/awsf/",
"launch_instance": True,
"password": "******",
"log_bucket": "tibanna-output",
"key_name": ""
},
}
data.update(
_tibanna_settings({
'run_id': str(object_key),
'run_type': workflow,
'env': env,
}))
return data