def setup(args):
template, template_txt = name_to_config(args.template)
base_item = template["details"][0]
project_name, metadata, global_vars = _pname_and_metadata(args.metadata)
remotes = _retrieve_remote([args.template, args.metadata])
inputs = args.input_files + remotes.get("inputs", [])
items = [
_add_metadata(item, metadata, remotes)
for item in _prep_items_from_base(base_item, inputs)
]
out_dir = os.path.join(os.getcwd(), project_name)
work_dir = utils.safe_makedir(os.path.join(out_dir, "work"))
if len(items) == 0:
out_config_file = _write_template_config(template_txt, project_name,
out_dir)
print "Template configuration file created at: %s" % out_config_file
print "Edit to finalize custom options, then prepare full sample config with:"
print " bcbio_nextgen.py -w template %s %s sample1.bam sample2.fq" % \
(out_config_file, project_name)
else:
out_config_file = _write_config_file(items, global_vars, template,
project_name, out_dir)
print "Configuration file created at: %s" % out_config_file
print "Edit to finalize and run with:"
print " cd %s" % work_dir
print " bcbio_nextgen.py ../config/%s" % os.path.basename(
out_config_file)
if remotes.get("base"):
remote_path = os.path.join(remotes["base"],
os.path.basename(out_config_file))
bucket, key = utils.s3_bucket_key(remote_path)
s3.upload_file_boto(out_config_file, bucket, key)
print "Also uploaded to AWS S3 in %s" % remotes["base"]
print "Run directly with bcbio_vm.py run %s" % remote_path
def setup(args):
template, template_txt = name_to_config(args.template)
base_item = template["details"][0]
project_name, metadata, global_vars = _pname_and_metadata(args.metadata)
remotes = _retrieve_remote([args.template, args.metadata])
inputs = args.input_files + remotes.get("inputs", [])
items = [_add_metadata(item, metadata, remotes)
for item in _prep_items_from_base(base_item, inputs)]
out_dir = os.path.join(os.getcwd(), project_name)
work_dir = utils.safe_makedir(os.path.join(out_dir, "work"))
if len(items) == 0:
out_config_file = _write_template_config(template_txt, project_name, out_dir)
print "Template configuration file created at: %s" % out_config_file
print "Edit to finalize custom options, then prepare full sample config with:"
print " bcbio_nextgen.py -w template %s %s sample1.bam sample2.fq" % \
(out_config_file, project_name)
else:
out_config_file = _write_config_file(items, global_vars, template, project_name, out_dir)
print "Configuration file created at: %s" % out_config_file
print "Edit to finalize and run with:"
print " cd %s" % work_dir
print " bcbio_nextgen.py ../config/%s" % os.path.basename(out_config_file)
if remotes.get("base"):
remote_path = os.path.join(remotes["base"], os.path.basename(out_config_file))
bucket, key = utils.s3_bucket_key(remote_path)
s3.upload_file_boto(out_config_file, bucket, key)
print "Also uploaded to AWS S3 in %s" % remotes["base"]
print "Run directly with bcbio_vm.py run %s" % remote_path
def setup(args):
template, template_txt = name_to_config(args.template)
base_item = template["details"][0]
project_name, metadata, global_vars, md_file = _pname_and_metadata(args.metadata)
remotes = _retrieve_remote([args.metadata, args.template])
inputs = args.input_files + remotes.get("inputs", [])
raw_items = [
_add_metadata(item, metadata, remotes, args.only_metadata) for item in _prep_items_from_base(base_item, inputs)
]
items = [x for x in raw_items if x]
_check_all_metadata_found(metadata, items)
out_dir = os.path.join(os.getcwd(), project_name)
work_dir = utils.safe_makedir(os.path.join(out_dir, "work"))
if hasattr(args, "relpaths") and args.relpaths:
items = [_convert_to_relpaths(x, work_dir) for x in items]
out_config_file = _write_template_config(template_txt, project_name, out_dir)
if md_file:
shutil.copyfile(md_file, os.path.join(out_dir, "config", os.path.basename(md_file)))
if len(items) == 0:
print
print "Template configuration file created at: %s" % out_config_file
print "Edit to finalize custom options, then prepare full sample config with:"
print " bcbio_nextgen.py -w template %s %s sample1.bam sample2.fq" % (out_config_file, project_name)
else:
out_config_file = _write_config_file(items, global_vars, template, project_name, out_dir, remotes)
print
print "Configuration file created at: %s" % out_config_file
print "Edit to finalize and run with:"
print " cd %s" % work_dir
print " bcbio_nextgen.py ../config/%s" % os.path.basename(out_config_file)
if remotes.get("base"):
remote_path = os.path.join(remotes["base"], os.path.basename(out_config_file))
s3.upload_file_boto(out_config_file, remote_path)
print "Also uploaded to AWS S3 in %s" % remotes["base"]
print "Run directly with bcbio_vm.py run %s" % remote_path
def setup(args):
template, template_txt = name_to_config(args.template)
run_info.validate_yaml(template_txt, args.template)
base_item = template["details"][0]
project_name, metadata, global_vars, md_file = _pname_and_metadata(
args.metadata)
remotes = _retrieve_remote([args.metadata, args.template])
inputs = args.input_files + remotes.get(
"inputs", []) + [fr for fr in metadata if objectstore.is_remote(fr)]
if hasattr(args, "systemconfig") and args.systemconfig and hasattr(
args, "integrations"):
config, _ = config_utils.load_system_config(args.systemconfig)
for iname, retriever in args.integrations.items():
if iname in config:
inputs += retriever.get_files(metadata, config[iname])
raw_items = [
_add_metadata(item, metadata, remotes, args.only_metadata)
for item in _prep_items_from_base(base_item, inputs, args.force_single)
]
items = [x for x in raw_items if x]
_check_all_metadata_found(metadata, items)
out_dir = os.path.join(os.getcwd(), project_name)
work_dir = utils.safe_makedir(os.path.join(out_dir, "work"))
if hasattr(args, "relpaths") and args.relpaths:
items = [_convert_to_relpaths(x, work_dir) for x in items]
out_config_file = _write_template_config(template_txt, project_name,
out_dir)
if md_file:
shutil.copyfile(
md_file, os.path.join(out_dir, "config",
os.path.basename(md_file)))
items = _copy_to_configdir(items, out_dir)
if len(items) == 0:
print()
print("Template configuration file created at: %s" % out_config_file)
print(
"Edit to finalize custom options, then prepare full sample config with:"
)
print(" bcbio_nextgen.py -w template %s %s sample1.bam sample2.fq" % \
(out_config_file, project_name))
else:
out_config_file = _write_config_file(items, global_vars, template,
project_name, out_dir, remotes)
print()
print("Configuration file created at: %s" % out_config_file)
print("Edit to finalize and run with:")
print(" cd %s" % work_dir)
print(" bcbio_nextgen.py ../config/%s" %
os.path.basename(out_config_file))
if remotes.get("base"):
remote_path = os.path.join(remotes["base"],
os.path.basename(out_config_file))
s3.upload_file_boto(out_config_file, remote_path)
print("Also uploaded to AWS S3 in %s" % remotes["base"])
print("Run directly with bcbio_vm.py run %s" % remote_path)
def setup(args):
template, template_txt = name_to_config(args.template)
run_info.validate_yaml(template_txt, args.template)
base_item = template["details"][0]
project_name, metadata, global_vars, md_file = _pname_and_metadata(args.metadata)
remotes = _retrieve_remote([args.metadata, args.template])
inputs = args.input_files + remotes.get("inputs", []) + _find_remote_inputs(metadata)
remote_retriever = None
remote_config = None
if hasattr(args, "systemconfig") and args.systemconfig and hasattr(args, "integrations"):
config, _ = config_utils.load_system_config(args.systemconfig)
for iname, retriever in args.integrations.items():
if iname in config:
remote_retriever = retriever
remote_config = remote_retriever.set_cache(config[iname])
inputs += remote_retriever.get_files(metadata, remote_config)
raw_items = [_add_metadata(item, metadata, remotes, args.only_metadata)
for item in _prep_items_from_base(base_item, inputs, metadata,
args.separators.split(","), args.force_single)]
items = [x for x in raw_items if x]
_check_all_metadata_found(metadata, items)
if remote_retriever and remote_config:
items = remote_retriever.add_remotes(items, remote_config)
out_dir = os.path.join(os.getcwd(), project_name)
work_dir = utils.safe_makedir(os.path.join(out_dir, "work"))
if hasattr(args, "relpaths") and args.relpaths:
items = [_convert_to_relpaths(x, work_dir) for x in items]
out_config_file = _write_template_config(template_txt, project_name, out_dir)
if md_file:
shutil.copyfile(md_file, os.path.join(out_dir, "config", os.path.basename(md_file)))
items = _copy_to_configdir(items, out_dir)
if len(items) == 0:
print()
print("Template configuration file created at: %s" % out_config_file)
print("Edit to finalize custom options, then prepare full sample config with:")
print(" bcbio_nextgen.py -w template %s %s sample1.bam sample2.fq" % \
(out_config_file, project_name))
else:
out_config_file = _write_config_file(items, global_vars, template, project_name, out_dir,
remotes)
print()
print("Configuration file created at: %s" % out_config_file)
print("Edit to finalize and run with:")
print(" cd %s" % work_dir)
print(" bcbio_nextgen.py ../config/%s" % os.path.basename(out_config_file))
if remotes.get("base"):
remote_path = os.path.join(remotes["base"], os.path.basename(out_config_file))
s3.upload_file_boto(out_config_file, remote_path)
print("Also uploaded to AWS S3 in %s" % remotes["base"])
print("Run directly with bcbio_vm.py run %s" % remote_path)
def setup(args):
template, template_txt = name_to_config(args.template)
base_item = template["details"][0]
project_name, metadata, global_vars, md_file = _pname_and_metadata(
args.metadata)
remotes = _retrieve_remote([args.metadata, args.template])
inputs = args.input_files + remotes.get("inputs", [])
raw_items = [
_add_metadata(item, metadata, remotes, args.only_metadata)
for item in _prep_items_from_base(base_item, inputs)
]
items = [x for x in raw_items if x]
_check_all_metadata_found(metadata, items)
out_dir = os.path.join(os.getcwd(), project_name)
work_dir = utils.safe_makedir(os.path.join(out_dir, "work"))
if hasattr(args, "relpaths") and args.relpaths:
items = [_convert_to_relpaths(x, work_dir) for x in items]
out_config_file = _write_template_config(template_txt, project_name,
out_dir)
if md_file:
shutil.copyfile(
md_file, os.path.join(out_dir, "config",
os.path.basename(md_file)))
if len(items) == 0:
print
print "Template configuration file created at: %s" % out_config_file
print "Edit to finalize custom options, then prepare full sample config with:"
print " bcbio_nextgen.py -w template %s %s sample1.bam sample2.fq" % \
(out_config_file, project_name)
else:
out_config_file = _write_config_file(items, global_vars, template,
project_name, out_dir, remotes)
print
print "Configuration file created at: %s" % out_config_file
print "Edit to finalize and run with:"
print " cd %s" % work_dir
print " bcbio_nextgen.py ../config/%s" % os.path.basename(
out_config_file)
if remotes.get("base"):
remote_path = os.path.join(remotes["base"],
os.path.basename(out_config_file))
s3.upload_file_boto(out_config_file, remote_path)
print "Also uploaded to AWS S3 in %s" % remotes["base"]
print "Run directly with bcbio_vm.py run %s" % remote_path
