def run_preflight_checks(args):
print "Checking sample info..."
cr_preflight.check_sample_def(args.sample_def)
print "Checking reference..."
cr_preflight.check_refdata(args.reference_path)
print "Checking chemistry..."
cr_preflight.check_chemistry(args.chemistry_name, args.custom_chemistry_def,
args.allowed_chems)
if args.r1_length is not None:
print "Checking read 1 length..."
cr_preflight.check_read_length(args.r1_length)
if args.r2_length is not None:
print "Checking read 2 length..."
cr_preflight.check_read_length(args.r2_length)
# Open file handles limit - per CELLRANGER-824, only check this on the execution machine.
# We can tell if we're on the execution machine by looking at args.check_executables
if args.check_executables:
print "Checking system environment..."
cr_preflight.check_environment()
print "Checking optional arguments..."
if args.recovered_cells is not None and args.force_cells is not None:
raise cr_preflight.PreflightException("Cannot specify both --force-cells and --expect-cells in the same run.")
def run_preflight_checks(args):
if args.feature_reference is not None:
print "Checking feature definition file..."
feature_ref = cr_preflight.check_feature_ref(args.reference_path,
args.feature_reference)
else:
feature_ref = None
print "Checking sample info..."
cr_preflight.check_sample_def(args.sample_def,
feature_ref,
pipeline=PIPELINE_COUNT)
# If any non "Gene Expression" libraries are present then the feature-ref is required.
if any((x.get("library_type") != None
and x.get("library_type") != GENE_EXPRESSION_LIBRARY_TYPE)
for x in args.sample_def):
if args.feature_reference is None:
raise cr_preflight.PreflightException(
"You must specify --feature-ref when using Cell Ranger with feature barcoding libraries."
)
# At least one "Gene Expression" library is required.
# Treat an empty library_type as GENE_EXPRESSION
if not any(
x.get("library_type") == GENE_EXPRESSION_LIBRARY_TYPE
or x.get("library_type") == None for x in args.sample_def):
raise cr_preflight.PreflightException(
"You must specify >= 1 input library with library_type == '%s' to run 'cellranger count'"
% GENE_EXPRESSION_LIBRARY_TYPE)
print "Checking reference..."
cr_preflight.check_refdata(args.reference_path)
print "Checking chemistry..."
cr_preflight.check_chemistry(args.chemistry_name,
args.custom_chemistry_def, args.allowed_chems)
if args.r1_length is not None:
print "Checking read 1 length..."
cr_preflight.check_read_length(args.r1_length)
if args.r2_length is not None:
print "Checking read 2 length..."
cr_preflight.check_read_length(args.r2_length)
# Open file handles limit - per CELLRANGER-824, only check this on the execution machine.
# We can tell if we're on the execution machine by looking at args.check_executables
if args.check_executables:
print "Checking system environment..."
cr_preflight.check_environment()
print "Checking optional arguments..."
if args.recovered_cells is not None and args.force_cells is not None:
raise cr_preflight.PreflightException(
"Cannot specify both --force-cells and --expect-cells in the same run."
)
def run_preflight_checks(args):
print "Checking sample info..."
cr_preflight.check_sample_def(args.sample_def)
# Don't check the GEX reference if we are just distinguishing between SCVDJ seq configs
if 'SCVDJ' not in args.chemistry_name_spec:
print "Checking reference..."
cr_preflight.check_refdata(args.reference_path)
if args.vdj_reference_path is not None:
print "Checking V(D)J reference..."
vdj_preflight.check_refdata(args.vdj_reference_path, True)
def main(args, outs):
hostname = socket.gethostname()
print "Checking sample info..."
ok, msg = tk_preflight.check_gem_groups(args.sample_def)
if not ok:
martian.exit(msg)
print "Checking FASTQ folder..."
for sample_def in args.sample_def:
read_path = sample_def["read_path"]
if not read_path.startswith('/'):
martian.exit(
"Specified FASTQ folder must be an absolute path: %s" %
read_path)
if not os.path.exists(read_path):
martian.exit(
"On machine: %s, specified FASTQ folder does not exist: %s" %
(hostname, read_path))
if not os.access(read_path, os.X_OK):
martian.exit(
"On machine: %s, cellranger does not have permission to open FASTQ folder: %s"
% (hostname, read_path))
if not os.listdir(read_path):
martian.exit("Specified FASTQ folder is empty: " + read_path)
lanes = sample_def["lanes"]
if lanes is not None:
for lane in lanes:
if not is_int(lane):
martian.exit(
"Lanes must be a comma-separated list of numbers.")
ok, msg = tk_preflight.check_sample_indices(sample_def)
if not ok:
martian.exit(msg)
if args.reference_path is None and args.vdj_reference_path is None:
martian.exit(
"Must specify either reference_path or vdj_reference_path.")
print "Checking transcriptome..."
if args.reference_path is not None:
ok, msg = cr_preflight.check_refdata(args.reference_path)
if not ok:
martian.exit(msg)
if args.vdj_reference_path is not None:
ok, msg = vdj_preflight.check_refdata(args.vdj_reference_path)
if not ok:
martian.exit(msg)
print "Checking chemistry..."
ok, msg = cr_chem.check_chemistry_defs()
if not ok:
martian.exit(msg)
ok, msg = cr_chem.check_chemistry_arg(args.chemistry_name)
if not ok:
martian.exit(msg)
if args.chemistry_name == cr_chem.CUSTOM_CHEMISTRY_NAME:
ok, msg = cr_chem.check_chemistry_def(args.custom_chemistry_def)
if not ok:
martian.exit(msg)
# Open file handles limit - per CELLRANGER-824, only check this on the execution machine.
# We can tell if we're on the execution machine by looking at args.check_executables
if args.check_executables:
print "Checking system environment..."
ok, msg = tk_preflight.check_open_fh()
if not ok:
martian.exit(msg)
print "Checking optional arguments..."
if args.recovered_cells is not None and args.force_cells is not None:
martian.exit(
"Cannot specify both --force-cells and --expect-cells (or --cells) in the same run."
)
cr_preflight.record_package_versions()