def test_shell_region2():
os.environ['AWS_DEFAULT_REGION'] = REGION2
res = API().run_workflow(input_json=get_test_json('shelltest4.json'),
sfn=DEV_SFN_REGION2)
jobid = res['jobid']
time.sleep(300)
status = API().check_status(job_id=jobid)
assert status == 'SUCCEEDED'
def test_shell():
os.environ['AWS_DEFAULT_REGION'] = REGION1
res = API().run_workflow(input_json=get_test_json('shelltest4.json'),
sfn=DEV_SFN_REGION1)
jobid = res['jobid']
time.sleep(300)
status = API().check_status(job_id=jobid)
status_costupdater = API().check_costupdater_status(job_id=jobid)
assert status_unicorn == 'SUCCEEDED' and status_costupdater == 'SUCCEEDED'
def test_cw_metrics_region2():
os.environ['AWS_DEFAULT_REGION'] = REGION2
res = API().run_workflow(
input_json=get_test_json('4dn_bwa.runonly.v1.json'),
sfn=DEV_SFN2_REGION2)
jobid = res['jobid']
time.sleep(60 * 20)
status = API().check_status(job_id=jobid)
assert status == 'SUCCEEDED'
prj = json.loads(API().log(job_id=jobid, postrunjson=True))
assert prj['metrics']['max_mem_utilization_percent']
assert prj['metrics']['max_cpu_utilization_percent']
def run_tibanna(num):
bucket = "eo72-4dn"
file_index = "{:02d}".format(num)
output = "PON_" + file_index
vcflist = "vcf" + file_index + ".list "
options = " --setKey \"null\" --filteredAreUncalled --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED"
command = "java -Xmx100g -jar /usr/GenomeAnalysisTK.jar -nt 16 -T CombineVariants -R GRCh38.d1.vd1.fa " + "--variant " + vcflist + options + " -o " + output + ".vcf.gz"
tibanna_args = {
"args": {
"language": "shell",
"command": [command],
"container_image": "broadinstitute/gatk3:3.8-1",
"output_S3_bucket": bucket,
"output_target": {
"file:///data1/shell/" + output + ".vcf.gz":
"PON/" + output + ".vcf.gz",
"file:///data1/shell/" + output + ".vcf.gz.tbi":
"PON/" + output + ".vcf.gz.tbi",
},
"input_files": {
"file:///data1/shell/VCFS/": "s3://eo72-4dn/vcfpass",
"file:///data1/shell/" + "GRCh38.d1.vd1.fa.fai": {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.fa.fai"
},
"file:///data1/shell/" + "GRCh38.d1.vd1.dict": {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.dict"
},
"file:///data1/shell/" + "GRCh38.d1.vd1.fa": {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.fa"
},
"file:///data1/shell/" + vcflist: {
"bucket_name": bucket,
"object_key": "vcflist/" + vcflist
}
}
},
"config": {
"instance_type": "r5.4xlarge",
"log_bucket": bucket,
"ebs_size": 60,
"EBS_optimized": True,
"behavior_on_capacity_limit": "wait_and_retry"
}
}
API().run_workflow(
input_json=tibanna_args) # json file or dictionary object
def run_tibanna(file, name):
command = "java -jar /usr/GenomeAnalysisTK.jar -T MuTect2 -R GRCh38.d1.vd1.fa -I:tumor " + file + " -o "+ name + ".vcf.gz"
tibanna_args = {
"args": {
"language": "shell",
"command": [ "pwd", "ls /", "ls /gatk/", command] ,
"container_image": "broadinstitute/gatk3:3.8-1",
"output_S3_bucket": bucket,
"output_target": {
"file:///data1/shell/" + name + ".vcf.gz" : "GATK3_MUTECT/" + name + ".vcf.gz",
"file:///data1/shell/" + name + ".vcf.gz.tbi" : "GATK3_MUTECT/" + name + ".vcf.gz.tbi"
},
"input_files": {
"file:///data1/shell/" + file : {
"bucket_name": bucket,
"object_key": path
},
"file:///data1/shell/" + name + ".bai" : {
"bucket_name": bucket,
"object_key": "output/" + name + ".bai"
},
"file:///data1/shell/" + "GRCh38.d1.vd1.fa.fai" : {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.fa.fai"
},
"file:///data1/shell/" + "GRCh38.d1.vd1.dict" : {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.dict"
},
"file:///data1/shell/" + "GRCh38.d1.vd1.fa" : {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.fa"
}
}
},
"config": {
"instance_type": "r4.large",
"log_bucket": bucket,
"ebs_size": 60,
"EBS_optimized" : True,
"behavior_on_capacity_limit": "wait_and_retry",
"spot_instance": True
}
}
API().run_workflow(input_json= tibanna_args) # json file or dictionary object
def cleanup_sfn2_region2():
os.environ['AWS_DEFAULT_REGION'] = REGION2
API().cleanup(user_group_name=DEV_GROUP_SUFFIX + '2', suffix=DEV_SUFFIX)
def deploy_sfn2_to_region2():
os.environ['AWS_DEFAULT_REGION'] = REGION2
buckets = 'tibanna-output,elasticbeanstalk-fourfront-webdev-files,soos-4dn-bucket'
API().deploy_unicorn(suffix=DEV_SUFFIX, buckets=buckets, usergroup=DEV_GROUP_SUFFIX + '2')
def deploy_sfn1_to_region2():
os.environ['AWS_DEFAULT_REGION'] = REGION2
API().deploy_unicorn(suffix=DEV_SUFFIX, buckets='tibanna-output,soos-4dn-bucket', usergroup=DEV_GROUP_SUFFIX + '1')
def deploy_sfn1_to_region1():
"""Deploy sfn1 to region1 with cost updater"""
os.environ['AWS_DEFAULT_REGION'] = REGION1
API().deploy_unicorn(suffix=DEV_SUFFIX, buckets='tibanna-output,soos-4dn-bucket', usergroup=DEV_GROUP_SUFFIX + '1',
deploy_costupdater = True)
"PON/" + output + ".vcf.gz",
"file:///data1/shell/" + output + ".vcf.gz.tbi":
"PON/" + output + ".vcf.gz.tbi"
},
"input_files": {
"file:///data1/shell/VCFS/": "s3://eo72-4dn/PON_1000",
"file:///data1/shell/" + "GRCh38.d1.vd1.fa.fai": {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.fa.fai"
},
"file:///data1/shell/" + "GRCh38.d1.vd1.dict": {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.dict"
},
"file:///data1/shell/" + "GRCh38.d1.vd1.fa": {
"bucket_name": bucket,
"object_key": "FASTA/GRCh38.d1.vd1.fa"
}
}
},
"config": {
"instance_type": "r5.4xlarge",
"log_bucket": bucket,
"ebs_size": 60,
"EBS_optimized": True,
"behavior_on_capacity_limit": "wait_and_retry"
}
}
API().run_workflow(input_json=tibanna_args) # json file or dictionary object
def run_tibanna(region):
path = "<PATH>"
bucket = "<BUCKET>"
format_region = "{:04d}".format(region)
regionfile = format_region + "-scattered.intervals"
tumor = path.split("/")[1]
out = tumor.split(".")[0] + "_" + format_region
command = "java -jar /usr/GenomeAnalysisTK.jar -T MuTect2 -R GRCh38_full_analysis_set_plus_decoy_hla.fa -L " + regionfile + " -I:tumor " + tumor + " -o "+ out + ".vcf.gz"
print(command)
tibanna_args = {
"args": {
"language": "shell",
"command": command ,
"container_image": "broadinstitute/gatk3:3.8-1",
"output_S3_bucket": bucket,
"output_target": {
"file:///data1/shell/" + out + ".vcf.gz" : "WGS/"+ tumor.split(".")[0]+ "/" + out + ".vcf.gz",
"file:///data1/shell/" + out + ".vcf.gz.tbi" : "WGS/"+ tumor.split(".")[0]+ "/" + out + ".vcf.gz.tbi"
},
"input_files": {
"file:///data1/shell/" + tumor : {
"bucket_name": bucket,
"object_key": path
},
"file:///data1/shell/" + tumor + ".bai" : {
"bucket_name": bucket,
"object_key": path + ".bai"
},
"file:///data1/shell/" + regionfile: {
"bucket_name": bucket,
"object_key": "regions/" + regionfile
},
"file:///data1/shell/" + "GRCh38_full_analysis_set_plus_decoy_hla.fa" : {
"bucket_name": bucket,
"object_key": "WGS/GRCh38_full_analysis_set_plus_decoy_hla.fa"
},
"file:///data1/shell/" + "GRCh38_full_analysis_set_plus_decoy_hla.dict" : {
"bucket_name": bucket,
"object_key": "WGS/GRCh38_full_analysis_set_plus_decoy_hla.dict"
},
"file:///data1/shell/" + "GRCh38_full_analysis_set_plus_decoy_hla.fa.fai" : {
"bucket_name": bucket,
"object_key": "WGS/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai"
}
}
},
"config": {
"instance_type": "r4.large",
"log_bucket": bucket,
"ebs_size": 150,
"EBS_optimized" : True,
"behavior_on_capacity_limit": "wait_and_retry"
}
}
print(json.dumps(tibanna_args, indent = 4))
API().run_workflow(input_json= tibanna_args)
