def run_gen(args):
syn = synapseclient.Synapse()
syn.login()
docstore = from_url(args.out_base)
data_mapping = {
"db_snp": "dbsnp_132_b37.leftAligned.vcf",
"centromere": "centromere_hg19.bed",
"reference_genome": "Homo_sapiens_assembly19.fasta",
"cosmic": "b37_cosmic_v54_120711.vcf"
}
if args.ref_download:
syn_sync(syn, REFDATA_PROJECT, docstore, data_mapping.values())
dm = {}
for k, v in data_mapping.items():
hit = None
for a in docstore.filter(name=v):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (v))
dm[k] = {"uuid": hit}
if args.sample is not None:
sync_doc_dir(os.path.join(os.path.dirname(__file__), "..",
"testexomes"),
docstore,
filter=lambda x: x['donorId'] in args.sample)
else:
sync_doc_dir(
os.path.join(os.path.dirname(__file__), "..", "testexomes"),
docstore)
tumor_uuids = {}
normal_uuids = {}
for id, ent in docstore.filter(sampleType="tumour"):
tumor_uuids[ent['participant_id']] = id
for id, ent in docstore.filter(sampleType="normal"):
normal_uuids[ent['participant_id']] = id
mc3_workflow = GalaxyWorkflow(
ga_file="workflows/Galaxy-Workflow-MC3_Pipeline_Test.ga")
reference_id = None
for a in docstore.filter(name="Homo_sapiens_assembly19.fasta"):
reference_id = a[0]
tasks = TaskGroup()
for donor in tumor_uuids:
if donor in normal_uuids:
print "participant", donor
donor_name = None
for k, v in fake_metadata.items():
if v['participant_id'] == donor:
donor_name = k
workflow_dm = dict(dm)
workflow_dm['tumor_bam'] = {"uuid": tumor_uuids[donor]}
workflow_dm['normal_bam'] = {"uuid": normal_uuids[donor]}
task = GalaxyWorkflowTask(
"workflow_%s" % (donor),
mc3_workflow,
inputs=workflow_dm,
parameters={
"reheader_config": {
"platform":
"Illumina",
"center":
"OHSU",
"reference_genome":
"Homo_sapiens_assembly19.fasta",
"participant_uuid":
fake_metadata[donor_name]['participant_id'],
"disease_code":
fake_metadata[donor_name]['disease'],
"filedate":
datetime.datetime.now().strftime("%Y%m%d"),
"normal_analysis_uuid":
fake_metadata[donor_name]['normal']['uuid'],
"normal_bam_name":
fake_metadata[donor_name]['normal']['file_name'],
"normal_aliquot_uuid":
fake_metadata[donor_name]['normal']['aliquot_id'],
"normal_aliquot_barcode":
fake_metadata[donor_name]['normal']['barcode'],
"tumor_analysis_uuid":
fake_metadata[donor_name]['tumour']['uuid'],
"tumor_bam_name":
fake_metadata[donor_name]['tumour']['file_name'],
"tumor_aliquot_uuid":
fake_metadata[donor_name]['tumour']['aliquot_id'],
"tumor_aliquot_barcode":
fake_metadata[donor_name]['tumour']['barcode'],
}
},
tags=["donor:%s" % (donor)],
)
tasks.append(task)
if not os.path.exists("%s.tasks" % (args.out_base)):
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id),
"w") as handle:
handle.write(json.dumps(data.to_dict()))
if args.create_service:
service = GalaxyService(docstore=docstore,
galaxy=args.galaxy,
sudo=args.sudo,
tool_data=args.tool_data,
tool_dir=args.tool_dir,
work_dir=args.work_dir,
smp=[["gatk_bqsr", 12], ["gatk_indel", 24],
["MuSE", 8], ["pindel", 8], ["mutect", 8],
["delly", 4], ["gatk_bqsr", 12],
["gatk_indel", 12], ["bwa_mem", 12],
["radia", 8], ['radia_filter', 8]])
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)
def run_gen(args):
syn = synapseclient.Synapse()
syn.login()
if args.alt_table is not None:
config['table_id'] = args.alt_table
docstore = from_url(args.out_base)
if args.ref_download:
#download reference files from Synapse and populate the document store
for a in syn.chunkedQuery('select * from entity where parentId=="%s"' % (REFDATA_PROJECT)):
ent = syn.get(a['entity.id'])
id = ent.annotations['uuid'][0]
t = Target(uuid=id)
docstore.create(t)
path = docstore.get_filename(t)
name = ent.name
if 'dataPrep' in ent.annotations:
if ent.annotations['dataPrep'][0] == 'gunzip':
subprocess.check_call("gunzip -c %s > %s" % (ent.path, path), shell=True)
name = name.replace(".gz", "")
else:
print "Unknown DataPrep"
else:
shutil.copy(ent.path, path)
docstore.update_from_file(t)
meta = {}
meta['name'] = name
meta['uuid'] = id
if 'dataPrep' in meta:
del meta['dataPrep']
docstore.put(id, meta)
data_mapping = {
"dbsnp" : "dbsnp_132_b37.leftAligned.vcf",
"cosmic" : "b37_cosmic_v54_120711.vcf",
"gold_indels" : "Mills_and_1000G_gold_standard.indels.hg19.sites.fixed.vcf",
"phase_one_indels" : "1000G_phase1.indels.hg19.sites.fixed.vcf"
}
dm = {}
for k,v in data_mapping.items():
hit = None
for a in docstore.filter(name=v):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (v))
dm[k] = { "uuid" : hit }
workflow_2 = GalaxyWorkflow(ga_file="workflows/Galaxy-Workflow-GATK_CGHub_2.ga")
workflow_3 = GalaxyWorkflow(ga_file="workflows/Galaxy-Workflow-GATK_CGHub_3.ga")
ref_rename = {
"HG19_Broad_variant" : "Homo_sapiens_assembly19"
}
tasks = TaskGroup()
for ent in synqueue.listAssignments(syn, **config):
bam_set = list( a[1] for a in ent['meta'].items() if a[0].startswith("id_") and isinstance(a[1], basestring) )
ref_set = set( a[1] for a in ent['meta'].items() if a[0].startswith("ref_assembly_") and isinstance(a[1], basestring) )
assert(len(ref_set) == 1)
ref_name = ref_set.pop()
if ref_name in ref_rename:
ref_name = ref_rename[ref_name]
hit = None
for a in docstore.filter(name=ref_name + ".fasta"):
hit = a[0]
for a in docstore.filter(name=ref_name + ".fa"):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (ref_name))
workflow_dm = dict(dm)
workflow_dm['reference_genome'] = { "uuid" : hit }
if len(bam_set) == 2:
task = GalaxyWorkflowTask("workflow_%s" % (ent['id']),
workflow_2,
inputs=workflow_dm,
parameters={
'INPUT_BAM_1' : {
"uuid" : bam_set[0],
"gnos_endpoint" : "cghub.ucsc.edu",
"cred_file" : "/tool_data/files/cghub.key"
},
'INPUT_BAM_2' : {
"uuid" : bam_set[1],
"gnos_endpoint" : "cghub.ucsc.edu",
"cred_file" : "/tool_data/files/cghub.key"
}
},
tags=[ "donor:%s" % (ent['meta']['participant_id']) ],
tool_tags = {
"BQSR_1" : {
"output_bam" : [ "original_bam:%s" % (bam_set[0]) ]
},
"BQSR_2" : {
"output_bam" : [ "original_bam:%s" % (bam_set[1]) ]
}
}
)
tasks.append(task)
elif len(bam_set) == 3:
task = GalaxyWorkflowTask("workflow_%s" % (ent['id']),
workflow_3,
inputs=workflow_dm,
parameters={
'INPUT_BAM_1' : {
"uuid" : bam_set[0],
"gnos_endpoint" : "cghub.ucsc.edu",
"cred_file" : "/tool_data/files/cghub.key"
},
'INPUT_BAM_2' : {
"uuid" : bam_set[1],
"gnos_endpoint" : "cghub.ucsc.edu",
"cred_file" : "/tool_data/files/cghub.key"
},
'INPUT_BAM_3' : {
"uuid" : bam_set[2],
"gnos_endpoint" : "cghub.ucsc.edu",
"cred_file" : "/tool_data/files/cghub.key"
}
},
tags=[ "donor:%s" % (ent['meta']['participant_id']) ],
tool_tags = {
"BQSR_1" : {
"output_bam" : [ "original_bam:%s" % (bam_set[0]) ]
},
"BQSR_2" : {
"output_bam" : [ "original_bam:%s" % (bam_set[1]) ]
},
"BQSR_3" : {
"output_bam" : [ "original_bam:%s" % (bam_set[2]) ]
}
}
)
tasks.append(task)
if not os.path.exists("%s.tasks" % (args.out_base)):
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id), "w") as handle:
handle.write(json.dumps(data.to_dict()))
if args.create_service:
service = GalaxyService(
docstore=docstore,
galaxy="bgruening/galaxy-stable",
sudo=True,
tool_data=args.tool_data,
tool_dir=args.tool_dir,
work_dir=args.work_dir,
smp=[
["gatk_bqsr", 12],
["gatk_indel", 24]
]
)
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)
def run_gen(args):
syn = synapseclient.Synapse()
syn.login()
docstore = from_url(args.out_base)
data_mapping = {
"db_snp" : "dbsnp_132_b37.leftAligned.vcf",
"centromere" : "centromere_hg19.bed",
"reference_genome" : "Homo_sapiens_assembly19.fasta",
"cosmic" : "b37_cosmic_v54_120711.vcf"
}
if args.ref_download:
syn_sync(syn, REFDATA_PROJECT, docstore, data_mapping.values())
dm = {}
for k,v in data_mapping.items():
hit = None
for a in docstore.filter(name=v):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (v))
dm[k] = { "uuid" : hit }
if args.sample is not None:
sync_doc_dir(
os.path.join( os.path.dirname(__file__), "..", "testexomes" ), docstore,
filter=lambda x: x['donorId'] in args.sample
)
else:
sync_doc_dir( os.path.join( os.path.dirname(__file__), "..", "testexomes" ), docstore)
tumor_uuids = {}
normal_uuids = {}
for id, ent in docstore.filter(sampleType="tumour"):
tumor_uuids[ent['participant_id']] = id
for id, ent in docstore.filter(sampleType="normal"):
normal_uuids[ent['participant_id']] = id
mc3_workflow = GalaxyWorkflow(ga_file="workflows/Galaxy-Workflow-MC3_Pipeline_Test.ga")
reference_id = None
for a in docstore.filter(name="Homo_sapiens_assembly19.fasta"):
reference_id = a[0]
tasks = TaskGroup()
for donor in tumor_uuids:
if donor in normal_uuids:
print "participant", donor
donor_name = None
for k,v in fake_metadata.items():
if v['participant_id'] == donor:
donor_name = k
workflow_dm = dict(dm)
workflow_dm['tumor_bam'] = { "uuid" : tumor_uuids[donor] }
workflow_dm['normal_bam'] = { "uuid" : normal_uuids[donor] }
task = GalaxyWorkflowTask("workflow_%s" % (donor),
mc3_workflow,
inputs=workflow_dm,
parameters={
"reheader_config" : {
"platform" : "Illumina",
"center" : "OHSU",
"reference_genome" : "Homo_sapiens_assembly19.fasta",
"participant_uuid" : fake_metadata[donor_name]['participant_id'],
"disease_code" : fake_metadata[donor_name]['disease'],
"filedate" : datetime.datetime.now().strftime("%Y%m%d"),
"normal_analysis_uuid" : fake_metadata[donor_name]['normal']['uuid'],
"normal_bam_name" : fake_metadata[donor_name]['normal']['file_name'],
"normal_aliquot_uuid" : fake_metadata[donor_name]['normal']['aliquot_id'],
"normal_aliquot_barcode": fake_metadata[donor_name]['normal']['barcode'],
"tumor_analysis_uuid" : fake_metadata[donor_name]['tumour']['uuid'],
"tumor_bam_name" : fake_metadata[donor_name]['tumour']['file_name'],
"tumor_aliquot_uuid" : fake_metadata[donor_name]['tumour']['aliquot_id'],
"tumor_aliquot_barcode" : fake_metadata[donor_name]['tumour']['barcode'],
}
},
tags=[ "donor:%s" % (donor) ],
)
tasks.append(task)
if not os.path.exists("%s.tasks" % (args.out_base)):
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id), "w") as handle:
handle.write(json.dumps(data.to_dict()))
if args.create_service:
service = GalaxyService(
docstore=docstore,
galaxy=args.galaxy,
sudo=args.sudo,
tool_data=args.tool_data,
tool_dir=args.tool_dir,
work_dir=args.work_dir,
smp=[
["gatk_bqsr", 12],
["gatk_indel", 24],
["MuSE", 8],
["pindel", 8],
["mutect", 8],
["delly", 4],
["gatk_bqsr", 12],
["gatk_indel", 12],
["bwa_mem", 12],
["radia", 8],
['radia_filter', 8]
]
)
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)
def run_gen(args):
syn = synapseclient.Synapse()
syn.login()
docstore = from_url(args.out_base)
data_mapping = {
"db_snp" : "dbsnp_132_b37.leftAligned.vcf",
"centromere" : "centromere_hg19.bed",
"cosmic" : "b37_cosmic_v54_120711.vcf"
}
ref_genomes = [
"Homo_sapiens_assembly19.fasta",
"GRCh37-lite.fa",
"GRCh37-lite-+-HPV_Redux-build.fa",
"GRCh37-lite_WUGSC_variant_1.fa.gz",
"GRCh37-lite_WUGSC_variant_2.fa.gz",
"hg19_M_rCRS.fa.gz"
]
if args.ref_download:
syn_sync(syn, REFDATA_PROJECT, docstore, data_mapping.values() + ref_genomes)
dm = {}
for k,v in data_mapping.items():
hit = None
for a in docstore.filter(name=v):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (v))
dm[k] = { "uuid" : hit }
mc3_dna_workflow = GalaxyWorkflow(ga_file="workflows/Galaxy-Workflow-MC3_Pipeline_CGHub_DNA.ga")
mc3_dnarna_workflow = GalaxyWorkflow(ga_file="workflows/Galaxy-Workflow-MC3_Pipeline_CGHub_DNA_RNA.ga")
rna_hit = None
for a in docstore.filter(name="hg19_M_rCRS.fa"):
rna_hit = a[0]
tasks = TaskGroup()
assembly_hits = {}
with open(args.joblist) as handle:
reader = csv.DictReader(handle, delimiter="\t")
for row in reader:
if row['normal_assembly'] != row['tumor_assembly']:
print "Row Mispatch", row['normal_assembly'], row['tumor_assembly']
#raise Exception("Mismatch reference")
ref_name = row['normal_assembly']
if ref_name in ref_rename:
ref_name = ref_rename[ref_name]
if ref_name in assembly_hits:
hit = assembly_hits[ref_name]
else:
hit = None
for a in docstore.filter(name=ref_name + ".fasta"):
hit = a[0]
for a in docstore.filter(name=ref_name + ".fa"):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (ref_name))
assembly_hits[ref_name] = hit
workflow_dm = dict(dm)
workflow_dm['reference_genome'] = { "uuid" : hit }
params = {
'tumor_bam' : {
"uuid" : row['tumor_analysis_id'],
"gnos_endpoint" : "cghub.ucsc.edu",
"cred_file" : "/tool_data/files/cghub.key"
},
'normal_bam' : {
"uuid" : row['normal_analysis_id'],
"gnos_endpoint" : "cghub.ucsc.edu",
"cred_file" : "/tool_data/files/cghub.key"
},
"reheader_config" : {
"platform" : "Illumina",
"center" : "OHSU",
"reference_genome" : ref_name,
"participant_uuid" : row['participant_id'],
"disease_code" : row['disease'],
"filedate" : datetime.datetime.now().strftime("%Y%m%d"),
"normal_analysis_uuid" : row['normal_analysis_id'],
"normal_bam_name" : row['normal_filename'],
"normal_aliquot_uuid" : row['normal_aliquot_id'],
"normal_aliquot_barcode": row['normal_barcode'],
"tumor_analysis_uuid" : row['tumor_analysis_id'],
"tumor_bam_name" : row['tumor_filename'],
"tumor_aliquot_uuid" : row['tumor_aliquot_id'],
"tumor_aliquot_barcode" : row['tumor_barcode'],
}
}
if row['rna_analysis_id'] != "NA":
params['rna_tumor_bam'] = {
"uuid" : row['rna_analysis_id'],
"gnos_endpoint" : "cghub.ucsc.edu",
"cred_file" : "/tool_data/files/cghub.key"
}
workflow_dm['rna_reference_genome'] = { "uuid" : rna_hit }
task = GalaxyWorkflowTask("workflow_%s" % (row['job_id']),
mc3_dnarna_workflow,
inputs=workflow_dm,
parameters=params,
tags=[ "donor:%s" % (row['participant_id']) ],
)
else:
task = GalaxyWorkflowTask("workflow_%s" % (row['job_id']),
mc3_dna_workflow,
inputs=workflow_dm,
parameters=params,
tags=[ "donor:%s" % (row['participant_id']) ],
)
tasks.append(task)
if not os.path.exists("%s.tasks" % (args.out_base)):
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id), "w") as handle:
handle.write(json.dumps(data.to_dict()))
service = GalaxyService(
docstore=docstore,
galaxy=args.galaxy,
sudo=args.sudo,
tool_data=args.tool_data,
tool_dir=args.tool_dir,
work_dir=args.work_dir,
smp=[
["gatk_bqsr", 12],
["gatk_indel", 24],
["MuSE", 8],
["pindel", 8],
["mutect", 8],
["delly", 4],
["gatk_bqsr", 12],
["gatk_indel", 12],
["bwa_mem", 12],
["radia", 8],
['radia_filter', 8]
]
)
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)
def run_gen(args):
syn = synapseclient.Synapse()
syn.login()
docstore = from_url(args.out_base)
data_mapping = {
"db_snp": "dbsnp_132_b37.leftAligned.vcf",
"centromere": "centromere_hg19.bed",
"cosmic": "b37_cosmic_v54_120711.vcf",
}
ref_genomes = [
"Homo_sapiens_assembly19.fasta",
"GRCh37-lite.fa",
"GRCh37-lite-+-HPV_Redux-build.fa",
"GRCh37-lite_WUGSC_variant_1.fa.gz",
"GRCh37-lite_WUGSC_variant_2.fa.gz",
"hg19_M_rCRS.fa.gz",
]
if args.ref_download:
syn_sync(syn, REFDATA_PROJECT, docstore, data_mapping.values() + ref_genomes)
dm = {}
for k, v in data_mapping.items():
hit = None
for a in docstore.filter(name=v):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (v))
dm[k] = {"uuid": hit}
mc3_dna_workflow = GalaxyWorkflow(ga_file="workflows/Galaxy-Workflow-MC3_Pipeline_CGHub_DNA.ga")
mc3_dnarna_workflow = GalaxyWorkflow(ga_file="workflows/Galaxy-Workflow-MC3_Pipeline_CGHub_DNA_RNA.ga")
rna_hit = None
for a in docstore.filter(name="hg19_M_rCRS.fa"):
rna_hit = a[0]
tasks = TaskGroup()
assembly_hits = {}
with open(args.joblist) as handle:
reader = csv.DictReader(handle, delimiter="\t")
for row in reader:
if row["normal_assembly"] != row["tumor_assembly"]:
print "Row Mispatch", row["normal_assembly"], row["tumor_assembly"]
# raise Exception("Mismatch reference")
ref_name = row["normal_assembly"]
if ref_name in ref_rename:
ref_name = ref_rename[ref_name]
if ref_name in assembly_hits:
hit = assembly_hits[ref_name]
else:
hit = None
for a in docstore.filter(name=ref_name + ".fasta"):
hit = a[0]
for a in docstore.filter(name=ref_name + ".fa"):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (ref_name))
assembly_hits[ref_name] = hit
workflow_dm = dict(dm)
workflow_dm["reference_genome"] = {"uuid": hit}
params = {
"tumor_bam": {
"uuid": row["tumor_analysis_id"],
"gnos_endpoint": "cghub.ucsc.edu",
"cred_file": "/tool_data/files/cghub.key",
},
"normal_bam": {
"uuid": row["normal_analysis_id"],
"gnos_endpoint": "cghub.ucsc.edu",
"cred_file": "/tool_data/files/cghub.key",
},
"reheader_config": {
"platform": "Illumina",
"center": "OHSU",
"reference_genome": ref_name,
"participant_uuid": row["participant_id"],
"disease_code": row["disease"],
"filedate": datetime.datetime.now().strftime("%Y%m%d"),
"normal_analysis_uuid": row["normal_analysis_id"],
"normal_bam_name": row["normal_filename"],
"normal_aliquot_uuid": row["normal_aliquot_id"],
"normal_aliquot_barcode": row["normal_barcode"],
"tumor_analysis_uuid": row["tumor_analysis_id"],
"tumor_bam_name": row["tumor_filename"],
"tumor_aliquot_uuid": row["tumor_aliquot_id"],
"tumor_aliquot_barcode": row["tumor_barcode"],
},
}
if row["rna_analysis_id"] != "NA":
params["rna_tumor_bam"] = {
"uuid": row["rna_analysis_id"],
"gnos_endpoint": "cghub.ucsc.edu",
"cred_file": "/tool_data/files/cghub.key",
}
workflow_dm["rna_reference_genome"] = {"uuid": rna_hit}
task = GalaxyWorkflowTask(
"workflow_%s" % (row["job_id"]),
mc3_dnarna_workflow,
inputs=workflow_dm,
parameters=params,
tags=["donor:%s" % (row["participant_id"])],
)
else:
task = GalaxyWorkflowTask(
"workflow_%s" % (row["job_id"]),
mc3_dna_workflow,
inputs=workflow_dm,
parameters=params,
tags=["donor:%s" % (row["participant_id"])],
)
tasks.append(task)
if not os.path.exists("%s.tasks" % (args.out_base)):
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id), "w") as handle:
handle.write(json.dumps(data.to_dict()))
service = GalaxyService(
docstore=docstore,
galaxy=args.galaxy,
sudo=args.sudo,
tool_data=args.tool_data,
tool_dir=args.tool_dir,
work_dir=args.work_dir,
smp=[
["gatk_bqsr", 12],
["gatk_indel", 24],
["MuSE", 8],
["pindel", 8],
["mutect", 8],
["delly", 4],
["gatk_bqsr", 12],
["gatk_indel", 12],
["bwa_mem", 12],
["radia", 8],
["radia_filter", 8],
],
)
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)
def run_gen(args):
args = parser.parse_args()
syn = synapseclient.Synapse()
syn.login()
docstore = from_url(args.out_base)
data_mapping = {
"reference_genome": "genome.fa",
"dbsnp": "dbsnp_132_b37.leftAligned.vcf",
"cosmic": "b37_cosmic_v54_120711.vcf",
"gold_indels":
"Mills_and_1000G_gold_standard.indels.hg19.sites.fixed.vcf",
"phase_one_indels": "1000G_phase1.indels.hg19.sites.fixed.vcf",
"centromere": "centromere_hg19.bed"
}
if args.ref_download:
#download reference files from Synapse and populate the document store
for a in syn.chunkedQuery('select * from entity where parentId=="%s"' %
(REFDATA_PROJECT)):
print "found", a['entity.name']
if a['entity.name'] in data_mapping.values(
) or a['entity.name'].replace(".gz", "") in data_mapping.values():
print "loading"
ent = syn.get(a['entity.id'])
id = ent.annotations['uuid'][0]
t = Target(uuid=id)
docstore.create(t)
path = docstore.get_filename(t)
name = ent.name
if 'dataPrep' in ent.annotations:
if ent.annotations['dataPrep'][0] == 'gunzip':
subprocess.check_call("gunzip -c %s > %s" %
(ent.path, path),
shell=True)
name = name.replace(".gz", "")
else:
print "Unknown DataPrep"
else:
shutil.copy(ent.path, path)
docstore.update_from_file(t)
meta = {}
meta['name'] = name
meta['uuid'] = id
if 'dataPrep' in meta:
del meta['dataPrep']
docstore.put(id, meta)
dm = {}
for k, v in data_mapping.items():
hit = None
for a in docstore.filter(name=v):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (v))
dm[k] = {"uuid": hit}
workflow = GalaxyWorkflow(
ga_file="workflows/Galaxy-Workflow-PCAWG_CGHUB.ga")
tasks = TaskGroup()
for ent in synqueue.listAssignments(syn, **config):
#print "'%s'" % (ent['state']), ent['state'] == 'nan', type(ent['state']), type('nan')
if not isinstance(ent['state'], basestring) and isnan(ent['state']):
gnos_endpoint = urlparse(
ent['meta']['Normal_WGS_alignment_GNOS_repos']).netloc
task = GalaxyWorkflowTask(
"workflow_%s" % (ent['id']),
workflow,
inputs=dm,
parameters={
'normal_bam_download': {
"uuid":
ent['meta']['Normal_WGS_alignment_GNOS_analysis_ID'],
"gnos_endpoint":
gnos_endpoint,
"cred_file":
key_map[gnos_endpoint]
},
'tumor_bam_download': {
"uuid":
ent['meta']['Tumour_WGS_alignment_GNOS_analysis_IDs'],
"gnos_endpoint":
gnos_endpoint,
"cred_file":
key_map[gnos_endpoint]
},
'broad_variant_pipeline': {
"broad_ref_dir": "/tool_data/files/refdata",
"sample_id": ent['meta']['Submitter_donor_ID']
}
},
tags=["donor:%s" % (ent['meta']['Submitter_donor_ID'])])
tasks.append(task)
if not os.path.exists("%s.tasks" % (args.out_base)):
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id),
"w") as handle:
handle.write(json.dumps(data.to_dict()))
state_file = "%s.tasks/%s.state" % (args.out_base, data.task_id)
if os.path.exists(state_file):
os.unlink(state_file)
print "Tasks Created: %s" % (len(tasks))
if args.create_service:
service = GalaxyService(docstore=docstore,
galaxy="bgruening/galaxy-stable",
sudo=args.sudo,
tool_data=os.path.abspath("tool_data"),
tool_dir=os.path.abspath("tools"),
work_dir=args.work_dir,
smp=[["MuSE", 8], ["pindel", 8], ["muTect", 8],
["delly", 4], ["gatk_bqsr", 12],
["gatk_indel", 24], ["bwa_mem", 12],
["broad_variant_pipline", 24]])
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)
tags=[ "sample:%s" % (ent['meta']['Donor_ID']) ]
)
tasks.append(task)
if not os.path.exists("pcawg.tasks"):
os.mkdir("pcawg.tasks")
for data in tasks:
with open("pcawg.tasks/%s" % (data.task_id), "w") as handle:
handle.write(json.dumps(data.to_dict()))
if args.create_service:
service = GalaxyService(
docstore=docstore,
galaxy="bgruening/galaxy-stable:dev",
sudo=True,
tool_data=os.path.abspath("tool_data"),
tool_dir=os.path.abspath("tools"),
smp=[
["MuSE", 8],
["pindel", 8],
["muTect", 8],
["delly", 4],
["gatk_bqsr", 12],
["gatk_indel", 12],
["bwa_mem", 12],
["broad_variant_pipline", 28]
]
)
with open("pcawg.service", "w") as handle:
service.get_config().store(handle)
def run_gen(args):
syn = synapseclient.Synapse()
syn.login()
if args.alt_table is not None:
config['table_id'] = args.alt_table
docstore = from_url(args.out_base)
if args.ref_download:
#download reference files from Synapse and populate the document store
for a in syn.chunkedQuery('select * from entity where parentId=="%s"' %
(REFDATA_PROJECT)):
ent = syn.get(a['entity.id'])
id = ent.annotations['uuid'][0]
t = Target(uuid=id)
docstore.create(t)
path = docstore.get_filename(t)
name = ent.name
if 'dataPrep' in ent.annotations:
if ent.annotations['dataPrep'][0] == 'gunzip':
subprocess.check_call("gunzip -c %s > %s" %
(ent.path, path),
shell=True)
name = name.replace(".gz", "")
else:
print "Unknown DataPrep"
else:
shutil.copy(ent.path, path)
docstore.update_from_file(t)
meta = {}
meta['name'] = name
meta['uuid'] = id
if 'dataPrep' in meta:
del meta['dataPrep']
docstore.put(id, meta)
data_mapping = {
"dbsnp": "dbsnp_132_b37.leftAligned.vcf",
"cosmic": "b37_cosmic_v54_120711.vcf",
"gold_indels":
"Mills_and_1000G_gold_standard.indels.hg19.sites.fixed.vcf",
"phase_one_indels": "1000G_phase1.indels.hg19.sites.fixed.vcf"
}
dm = {}
for k, v in data_mapping.items():
hit = None
for a in docstore.filter(name=v):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (v))
dm[k] = {"uuid": hit}
workflow_2 = GalaxyWorkflow(
ga_file="workflows/Galaxy-Workflow-GATK_CGHub_2.ga")
workflow_3 = GalaxyWorkflow(
ga_file="workflows/Galaxy-Workflow-GATK_CGHub_3.ga")
ref_rename = {"HG19_Broad_variant": "Homo_sapiens_assembly19"}
tasks = TaskGroup()
for ent in synqueue.listAssignments(syn, **config):
bam_set = list(
a[1] for a in ent['meta'].items()
if a[0].startswith("id_") and isinstance(a[1], basestring))
ref_set = set(a[1] for a in ent['meta'].items()
if a[0].startswith("ref_assembly_")
and isinstance(a[1], basestring))
assert (len(ref_set) == 1)
ref_name = ref_set.pop()
if ref_name in ref_rename:
ref_name = ref_rename[ref_name]
hit = None
for a in docstore.filter(name=ref_name + ".fasta"):
hit = a[0]
for a in docstore.filter(name=ref_name + ".fa"):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (ref_name))
workflow_dm = dict(dm)
workflow_dm['reference_genome'] = {"uuid": hit}
if len(bam_set) == 2:
task = GalaxyWorkflowTask(
"workflow_%s" % (ent['id']),
workflow_2,
inputs=workflow_dm,
parameters={
'INPUT_BAM_1': {
"uuid": bam_set[0],
"gnos_endpoint": "cghub.ucsc.edu",
"cred_file": "/tool_data/files/cghub.key"
},
'INPUT_BAM_2': {
"uuid": bam_set[1],
"gnos_endpoint": "cghub.ucsc.edu",
"cred_file": "/tool_data/files/cghub.key"
}
},
tags=["donor:%s" % (ent['meta']['participant_id'])],
tool_tags={
"BQSR_1": {
"output_bam": ["original_bam:%s" % (bam_set[0])]
},
"BQSR_2": {
"output_bam": ["original_bam:%s" % (bam_set[1])]
}
})
tasks.append(task)
elif len(bam_set) == 3:
task = GalaxyWorkflowTask(
"workflow_%s" % (ent['id']),
workflow_3,
inputs=workflow_dm,
parameters={
'INPUT_BAM_1': {
"uuid": bam_set[0],
"gnos_endpoint": "cghub.ucsc.edu",
"cred_file": "/tool_data/files/cghub.key"
},
'INPUT_BAM_2': {
"uuid": bam_set[1],
"gnos_endpoint": "cghub.ucsc.edu",
"cred_file": "/tool_data/files/cghub.key"
},
'INPUT_BAM_3': {
"uuid": bam_set[2],
"gnos_endpoint": "cghub.ucsc.edu",
"cred_file": "/tool_data/files/cghub.key"
}
},
tags=["donor:%s" % (ent['meta']['participant_id'])],
tool_tags={
"BQSR_1": {
"output_bam": ["original_bam:%s" % (bam_set[0])]
},
"BQSR_2": {
"output_bam": ["original_bam:%s" % (bam_set[1])]
},
"BQSR_3": {
"output_bam": ["original_bam:%s" % (bam_set[2])]
}
})
tasks.append(task)
if not os.path.exists("%s.tasks" % (args.out_base)):
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id),
"w") as handle:
handle.write(json.dumps(data.to_dict()))
if args.create_service:
service = GalaxyService(docstore=docstore,
galaxy="bgruening/galaxy-stable",
sudo=True,
tool_data=args.tool_data,
tool_dir=args.tool_dir,
work_dir=args.work_dir,
smp=[["gatk_bqsr", 12], ["gatk_indel", 24]])
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id), "w") as handle:
handle.write(json.dumps(data.to_dict()))
if args.create_service:
service = GalaxyService(
docstore=docstore,
galaxy="bgruening/galaxy-stable",
sudo=True,
tool_data=os.path.abspath("tool_data"),
tool_dir=os.path.abspath("tools"),
smp=[
["MuSE", 8],
["pindel", 8],
["muTect", 8],
["delly", 4],
["gatk_bqsr", 12],
["gatk_indel", 24],
["bwa_mem", 12],
["broad_variant_pipline", 24]
]
)
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)
def run_gen(args):
args = parser.parse_args()
syn = synapseclient.Synapse()
syn.login()
docstore = from_url(args.out_base)
data_mapping = {
"reference_genome" : "genome.fa",
"dbsnp" : "dbsnp_132_b37.leftAligned.vcf",
"cosmic" : "b37_cosmic_v54_120711.vcf",
"gold_indels" : "Mills_and_1000G_gold_standard.indels.hg19.sites.fixed.vcf",
"phase_one_indels" : "1000G_phase1.indels.hg19.sites.fixed.vcf",
"centromere" : "centromere_hg19.bed"
}
if args.ref_download:
#download reference files from Synapse and populate the document store
for a in syn.chunkedQuery('select * from entity where parentId=="%s"' % (REFDATA_PROJECT)):
print "found", a['entity.name']
if a['entity.name'] in data_mapping.values() or a['entity.name'].replace(".gz", "") in data_mapping.values():
print "loading"
ent = syn.get(a['entity.id'])
id = ent.annotations['uuid'][0]
t = Target(uuid=id)
docstore.create(t)
path = docstore.get_filename(t)
name = ent.name
if 'dataPrep' in ent.annotations:
if ent.annotations['dataPrep'][0] == 'gunzip':
subprocess.check_call("gunzip -c %s > %s" % (ent.path, path), shell=True)
name = name.replace(".gz", "")
else:
print "Unknown DataPrep"
else:
shutil.copy(ent.path, path)
docstore.update_from_file(t)
meta = {}
meta['name'] = name
meta['uuid'] = id
if 'dataPrep' in meta:
del meta['dataPrep']
docstore.put(id, meta)
dm = {}
for k,v in data_mapping.items():
hit = None
for a in docstore.filter(name=v):
hit = a[0]
if hit is None:
raise Exception("%s not found" % (v))
dm[k] = { "uuid" : hit }
workflow = GalaxyWorkflow(ga_file="workflows/Galaxy-Workflow-PCAWG_CGHUB.ga")
tasks = TaskGroup()
for ent in synqueue.listAssignments(syn, **config):
#print "'%s'" % (ent['state']), ent['state'] == 'nan', type(ent['state']), type('nan')
if not isinstance(ent['state'], basestring) and isnan(ent['state']):
gnos_endpoint = urlparse(ent['meta']['Normal_WGS_alignment_GNOS_repos']).netloc
task = GalaxyWorkflowTask("workflow_%s" % (ent['id']),
workflow,
inputs=dm,
parameters={
'normal_bam_download' : {
"uuid" : ent['meta']['Normal_WGS_alignment_GNOS_analysis_ID'],
"gnos_endpoint" : gnos_endpoint,
"cred_file" : key_map[gnos_endpoint]
},
'tumor_bam_download' : {
"uuid" : ent['meta']['Tumour_WGS_alignment_GNOS_analysis_IDs'],
"gnos_endpoint" : gnos_endpoint,
"cred_file" : key_map[gnos_endpoint]
},
'broad_variant_pipeline' : {
"broad_ref_dir" : "/tool_data/files/refdata",
"sample_id" : ent['meta']['Submitter_donor_ID']
}
},
tags=[ "donor:%s" % (ent['meta']['Submitter_donor_ID']) ]
)
tasks.append(task)
if not os.path.exists("%s.tasks" % (args.out_base)):
os.mkdir("%s.tasks" % (args.out_base))
for data in tasks:
with open("%s.tasks/%s" % (args.out_base, data.task_id), "w") as handle:
handle.write(json.dumps(data.to_dict()))
state_file = "%s.tasks/%s.state" % (args.out_base, data.task_id)
if os.path.exists( state_file ):
os.unlink( state_file )
print "Tasks Created: %s" % (len(tasks))
if args.create_service:
service = GalaxyService(
docstore=docstore,
galaxy="bgruening/galaxy-stable",
sudo=args.sudo,
tool_data=os.path.abspath("tool_data"),
tool_dir=os.path.abspath("tools"),
work_dir=args.work_dir,
smp=[
["MuSE", 8],
["pindel", 8],
["muTect", 8],
["delly", 4],
["gatk_bqsr", 12],
["gatk_indel", 24],
["bwa_mem", 12],
["broad_variant_pipline", 24]
]
)
with open("%s.service" % (args.out_base), "w") as handle:
s = service.get_config()
if args.scratch:
print "Using scratch", args.scratch
s.set_docstore_config(cache_path=args.scratch, open_perms=True)
s.store(handle)