kwargs["config_file"] = global_config
kwargs["fc_dir"] = fc_dir
kwargs["run_info_yaml"] = run_info_yaml
return kwargs
if __name__ == "__main__":
kwargs = parse_cl_args(sys.argv[1:])
if "upgrade" in kwargs and kwargs["upgrade"]:
install.upgrade_bcbio(kwargs["args"])
elif "server" in kwargs and kwargs["server"]:
server_main.start(kwargs["args"])
elif "runfn" in kwargs and kwargs["runfn"]:
runfn.process(kwargs["args"])
elif "graph" in kwargs and kwargs["graph"]:
graph.bootstrap(kwargs["args"])
elif "version" in kwargs and kwargs["version"]:
programs.write_versions({"work": kwargs["args"].workdir})
elif "sequencer" in kwargs and kwargs["sequencer"]:
machine.check_and_postprocess(kwargs["args"])
else:
if kwargs.get("workflow"):
setup_info = workflow.setup(kwargs["workflow"],
kwargs.pop("inputs"))
if setup_info is None: # no automated run after setup
sys.exit(0)
workdir, new_kwargs = setup_info
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)
if kwargs.get("workflow"):
kwargs["inputs"] = inputs
kwargs["config_file"] = global_config
kwargs["fc_dir"] = fc_dir
kwargs["run_info_yaml"] = run_info_yaml
return kwargs
if __name__ == "__main__":
kwargs = parse_cl_args(sys.argv[1:])
if "upgrade" in kwargs and kwargs["upgrade"]:
install.upgrade_bcbio(kwargs["args"])
elif "server" in kwargs and kwargs["server"]:
server_main.start(kwargs["args"])
elif "runfn" in kwargs and kwargs["runfn"]:
runfn.process(kwargs["args"])
elif "graph" in kwargs and kwargs["graph"]:
graph.bootstrap(kwargs["args"])
elif "version" in kwargs and kwargs["version"]:
programs.write_versions({"work": kwargs["args"].workdir})
elif "sequencer" in kwargs and kwargs["sequencer"]:
machine.check_and_postprocess(kwargs["args"])
else:
if kwargs.get("workflow"):
setup_info = workflow.setup(kwargs["workflow"], kwargs.pop("inputs"))
if setup_info is None: # no automated run after setup
sys.exit(0)
workdir, new_kwargs = setup_info
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)
if paralleltype is None:
paralleltype = config_cores
if paralleltype is None:
paralleltype = "local"
if numcores is None:
numcores = 1
return paralleltype, int(numcores)
def _needed_workers(run_info):
"""Determine workers needed to run multiplex flowcells in parallel.
"""
names = []
for xs in run_info["details"]:
for x in xs:
names.append(x.get("name", (x["lane"], x["barcode_id"])))
return len(set(names))
if __name__ == "__main__":
kwargs = parse_cl_args(sys.argv[1:])
if kwargs["upgrade"]:
install.upgrade_bcbio(kwargs["args"])
else:
if kwargs["workflow"]:
setup_info = workflow.setup(kwargs["workflow"], kwargs["inputs"])
if setup_info is None: # no automated run after setup
sys.exit(0)
workdir, new_kwargs = setup_info
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)
numcores = 1
else:
numcores = _needed_workers(
get_run_info(fc_dir, config, run_info_yaml)[-1])
return paralleltype, int(numcores)
def _needed_workers(run_info):
"""Determine workers needed to run multiplex flowcells in parallel.
"""
names = []
for xs in run_info["details"]:
for x in xs:
names.append(x.get("name", (x["lane"], x["barcode_id"])))
return len(set(names))
if __name__ == "__main__":
kwargs = parse_cl_args(sys.argv[1:])
if kwargs["upgrade"]:
install.upgrade_bcbio(kwargs["args"])
else:
if kwargs["workflow"]:
setup_info = workflow.setup(kwargs["workflow"], kwargs["inputs"])
if setup_info is None: # no automated run after setup
sys.exit(0)
workdir, new_kwargs = setup_info
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)
for xs in run_info["details"]:
for x in xs:
names.append(x.get("name", (x["lane"], x["barcode_id"])))
return len(set(names))
def _upgrade_bcbio(method):
"""Perform upgrade of bcbio to latest release, or from GitHub development version.
"""
url = "https://raw.github.com/chapmanb/bcbio-nextgen/master/requirements.txt"
git_repo = "git://github.com/chapmanb/bcbio-nextgen.git"
pip_bin = os.path.join(os.path.dirname(sys.executable), "pip")
if method in ["stable", "system"]:
sudo_cmd = [] if method == "stable" else ["sudo"]
subprocess.check_call(sudo_cmd + [pip_bin, "install", "--upgrade", "distribute"])
subprocess.check_call(sudo_cmd + [pip_bin, "install", "-r", url])
else:
subprocess.check_call([pip_bin, "install", "--upgrade",
"git+%s#egg=bcbio-nextgen" % git_repo])
if __name__ == "__main__":
config_file, kwargs = parse_cl_args(sys.argv[1:])
kwargs["config_file"] = config_file
if kwargs["upgrade"] and config_file is None:
_upgrade_bcbio(kwargs["upgrade"])
else:
if kwargs["workflow"]:
workdir, new_kwargs = workflow.setup(kwargs["workflow"], kwargs["inputs"])
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)
"""
if "scheduler" in args and "queue" in args:
if args.scheduler and not args.queue:
if args.scheduler != "sge":
return "IPython parallel scheduler (-s) specified. This also requires a queue (-q)."
elif args.queue and not args.scheduler:
return "IPython parallel queue (-q) supplied. This also requires a scheduler (-s)."
elif args.paralleltype == "ipython" and (not args.queue
or not args.scheduler):
return "IPython parallel requires queue (-q) and scheduler (-s) arguments."
if __name__ == '__main__':
# sys.argv.extend(['upgrade' , '--tooldir', '/usr/local', '--genomes', 'GRCh37', '--aligners', 'bwa', '--aligners', 'bowtie2', '--data'])
sys.argv.extend([
'-w', 'template',
r'D:\python-projects\my_bcbio\config\gatk-variant.yaml', 'project1',
'sample1.bam', 'sample2_1.fq', 'sample2_2.fq'
])
# sys.argv.extend([ '-h'])
kwargs = parse_cl_args(sys.argv[1:])
if "upgrade" in kwargs and kwargs['upgrade']:
install.upgrade_bcbio(kwargs['args'])
else:
if kwargs.get("workflow"):
setup_info = workflow.setup(kwargs['workflow'],
kwargs.pop("inputs"))
print(kwargs)
def _upgrade_bcbio(method):
"""Perform upgrade of bcbio to latest release, or from GitHub development version.
"""
url = "https://raw.github.com/chapmanb/bcbio-nextgen/master/requirements.txt"
git_repo = "git://github.com/chapmanb/bcbio-nextgen.git"
pip_bin = os.path.join(os.path.dirname(sys.executable), "pip")
if method in ["stable", "system"]:
sudo_cmd = [] if method == "stable" else ["sudo"]
subprocess.check_call(sudo_cmd +
[pip_bin, "install", "--upgrade", "distribute"])
subprocess.check_call(sudo_cmd + [pip_bin, "install", "-r", url])
else:
subprocess.check_call([
pip_bin, "install", "--upgrade",
"git+%s#egg=bcbio-nextgen" % git_repo
])
if __name__ == "__main__":
config_file, kwargs = parse_cl_args(sys.argv[1:])
kwargs["config_file"] = config_file
if kwargs["upgrade"] and config_file is None:
_upgrade_bcbio(kwargs["upgrade"])
else:
if kwargs["workflow"]:
workdir, new_kwargs = workflow.setup(kwargs["workflow"],
kwargs["inputs"])
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)