def test_benchmark_none1(self):
input_json = {
'input_size_in_bytes': {
'fastq1': 93520,
'fastq2': 97604,
'bwa_index': 3364568
}
}
with self.assertRaises(B.AppNameUnavailableException):
B.benchmark('some_weird_name', input_json, raise_error=True)
def test_benchmark6(self):
input_json = {'input_size_in_bytes': {'input_pairsam': 1000000000}}
res = B.benchmark('pairsam-markasdup', input_json)
print(res)
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 'r4.large'
def test_benchmark10(self):
input_json = {'input_size_in_bytes': {'input_pairs': 1000000000}}
res = B.benchmark('pairs-patch', input_json)
print(res)
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 't2.micro'
def test_benchmark7(self):
input_json = {'input_size_in_bytes': {'input_pairsam': 1000000000}}
res = B.benchmark('pairsam-filter', input_json)
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 't2.xlarge'
print(res)
def test_benchmark1(self):
res = B.benchmark('md5',
{'input_size_in_bytes': {
'input_file': 200000000
}})
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 't2.micro'
print(res)
def test_benchmark_none2(self):
input_json = {
'input_size_in_bytes': {
'fastq1': 93520,
'fastq2': 97604,
'bwa_index': 3364568
}
}
res = B.benchmark('some_weird_name', input_json)
assert res is None
def test_benchmark5(self):
input_json = {
'input_size_in_bytes': {
'input_pairsams': [1000000000, 2000000000, 3000000000]
},
'parameters': {
'nThreads': 32
}
}
res = B.benchmark('pairsam-merge', input_json)
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 'c4.8xlarge'
print(res)
def test_benchmark4(self):
res = B.benchmark(
'pairsam-parse-sort', {
'input_size_in_bytes': {
'bam': 1000000000
},
'parameters': {
'nThreads': 16
}
})
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 'c4.8xlarge'
print(res)
def test_benchmark2(self):
res = B.benchmark(
'fastqc-0-11-4-1', {
'input_size_in_bytes': {
'input_fastq': 20000000000
},
'parameters': {
'threads': 2
}
})
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 't2.medium'
print(res)
def test_benchmark9(self):
input_json = {
'input_size_in_bytes': {
'input_pairs': [1000000000, 2000000000, 3000000000]
},
'parameters': {
'ncores': 16,
'maxmem': '1900g'
}
}
res = B.benchmark('hi-c-processing-partb', input_json)
print(res)
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 'x1.32xlarge'
def test_benchmark3(self):
input_json = {
'input_size_in_bytes': {
'fastq1': 93520000,
'fastq2': 97604000,
'bwa_index': 3364568000
},
'parameters': {
'nThreads': 4
}
}
res = B.benchmark('bwa-mem', input_json)
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 't2.xlarge'
print(res)
def test_benchmark11(self):
input_json = {
'input_size_in_bytes': {
'input_cool': 1000000000,
'input_hic': 2000000000
},
'parameters': {
'ncores': 1
}
}
res = B.benchmark('hi-c-processing-partc', input_json)
print('hi-c-processing-partc')
print(res)
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 'r4.large'
def test_benchmark13(self):
input_json = {
'input_size_in_bytes': {
'input_pairs': [1000000000, 2000000000, 3000000000]
},
'parameters': {
'nthreads': 8,
'maxmem': '32g'
}
}
res = B.benchmark('hi-c-processing-pairs', input_json)
print('hi-c-processing-pairs')
print("benchmark13")
print(res)
assert 'aws' in res
assert res['min_CPU'] == 8
assert int(res['total_mem_in_MB']) == 45776
assert int(res['total_size_in_GB']) == 97
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 'r4.2xlarge'
def test_benchmark12(self):
input_json = {
'input_size_in_bytes': {
'input_bams': [1000000000, 2000000000],
'chromsize': 200000
},
'parameters': {
'nthreads_parse_sort': 1,
'nthreads_merge': 8
}
}
res = B.benchmark('hi-c-processing-bam', input_json)
print('hi-c-processing-bam')
print("benchmark12")
print(res)
assert 'aws' in res
assert 'recommended_instance_type' in res['aws']
assert res['aws']['recommended_instance_type'] == 't2.2xlarge'
assert res['min_CPU'] == 8
assert int(res['total_size_in_GB']) == 55
