import sys
from bcbio import install, workflow
from bcbio.illumina import machine
from bcbio.distributed import runfn
from bcbio.pipeline.main import run_main, parse_cl_args
from bcbio.server import main as server_main
from bcbio.provenance import programs
import pdb
def main(**kwargs):
run_main(**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 "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)
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)
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)
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))
def _upgrade_bcbio(method):
"""Perform upgrade of bcbio to latest release, or from GitHub development version.
"""
url = "https://raw.github.com/chapmanb/bcbb/master/nextgen/requirements.txt"
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:
raise NotImplementedError("Development upgrade")
if __name__ == "__main__":
config_file, kwargs = parse_cl_args(sys.argv[1:])
if kwargs["upgrade"] and config_file is None:
_upgrade_bcbio(kwargs["upgrade"])
else:
main(config_file, **kwargs)
