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