def full(args, dockerconf):
"""Full installaction of docker image and data.
"""
updates = []
args = add_install_defaults(args)
if args.wrapper:
updates.append("wrapper scripts")
upgrade_bcbio_vm()
dmounts = mounts.prepare_system(args.datadir, dockerconf["biodata_dir"])
if args.install_tools:
updates.append("bcbio-nextgen code and third party tools")
pull(args, dockerconf)
_check_docker_image(args)
# Ensure external galaxy configuration in sync when doing tool upgrade
manage.run_bcbio_cmd(args.image, dmounts, ["upgrade"])
if args.install_data:
if len(args.genomes) == 0:
print(
"Data not installed, no genomes provided with `--genomes` flag"
)
sys.exit(1)
elif len(args.aligners) == 0:
print(
"Data not installed, no aligners provided with `--aligners` flag"
)
sys.exit(1)
else:
updates.append("biological data")
if _check_docker_image(args, raise_error=False):
manage.run_bcbio_cmd(args.image, dmounts, _get_cl(args))
else:
args.upgrade = False
args.tools = False
args.tooldir = False
args.toolplus = False
args.isolate = True
args.distribution = None
args.cwl = True
print(args)
from bcbio import install
install.upgrade_bcbio(args)
_save_install_defaults(args)
if updates:
print("\nbcbio-nextgen-vm updated with latest %s" %
" and ".join(updates))
else:
print(
"\nNo update targets specified, need '--wrapper', '--tools' or '--data'\n"
"See 'bcbio_vm.py upgrade -h' for more details.")
def full(args, dockerconf):
"""Full installaction of docker image and data.
"""
updates = []
args = add_install_defaults(args)
if args.wrapper:
updates.append("wrapper scripts")
upgrade_bcbio_vm()
dmounts = mounts.prepare_system(args.datadir, dockerconf["biodata_dir"])
if args.install_tools:
updates.append("bcbio-nextgen code and third party tools")
pull(args, dockerconf)
_check_docker_image(args)
# Ensure external galaxy configuration in sync when doing tool upgrade
manage.run_bcbio_cmd(args.image, dmounts, ["upgrade"])
if args.install_data:
if len(args.genomes) == 0:
print("Data not installed, no genomes provided with `--genomes` flag")
sys.exit(1)
elif len(args.aligners) == 0:
print("Data not installed, no aligners provided with `--aligners` flag")
sys.exit(1)
else:
updates.append("biological data")
if _check_docker_image(args, raise_error=False):
manage.run_bcbio_cmd(args.image, dmounts, _get_cl(args))
else:
args.upgrade = False
args.tools = False
args.tooldir = False
args.toolplus = False
args.isolate = True
args.distribution = None
args.cwl = True
print(args)
from bcbio import install
install.upgrade_bcbio(args)
_save_install_defaults(args)
if updates:
print("\nbcbio-nextgen-vm updated with latest %s" % " and ".join(updates))
else:
print("\nNo update targets specified, need '--wrapper', '--tools' or '--data'\n"
"See 'bcbio_vm.py upgrade -h' for more details.")
sys.exit()
if fc_dir:
fc_dir = os.path.abspath(fc_dir)
if run_info_yaml:
run_info_yaml = os.path.abspath(run_info_yaml)
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)
if fc_dir:
fc_dir = os.path.abspath(fc_dir)
if run_info_yaml:
run_info_yaml = os.path.abspath(run_info_yaml)
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
"""
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)
