def _run_config_parser(argv):
'''Helper class for optparse.OptionParser
allows reading from and writing to a config file '''
per_host_cfg = PerHostConfig("epiPALEOMIX")
usage_str = "%prog <command> [options] [makefiles]"
version_str = "%%prog %s" % (__version__,)
parser = optparse.OptionParser(usage = __foreword__ + "\n" + usage_str,
version = version_str,
description = __description__,
epilog = __epilog__,
formatter=EpiPaleomixIndentHelper(),
prog="epiPALEOMIX")
pypeline.ui.add_optiongroup(parser,
ui_default=PerHostValue("quiet"),
color_default=PerHostValue("on"))
pypeline.logger.add_optiongroup(parser, default = PerHostValue("warning"))
parser.add_option("--max-threads", type = int, default = per_host_cfg.max_threads,
help = "Maximum number of threads to use in total [%default]")
parser.add_option("--dry-run", action = "store_true", default = False,
help = "If passed, only a dry-run in performed, the dependency "
"tree is printed, and no tasks are executed.")
parser.add_option("--temp-root", default = per_host_cfg.temp_root,
help = "Location for temporary files and folders [%default/]")
parser.add_option("--destination", default = './',
help = "The destination folder for result files. By default, "
"files will be placed in ./OUT_{makefile name}/")
parser.add_option("--list-output-files", action = "store_true", default = False,
help = "List all files generated by pipeline for the makefile(s).")
parser.add_option("--list-executables", action="store_true", default=False,
help="List all executables required by the pipeline, "
"with version requirements (if any).")
return per_host_cfg.parse_args(parser, argv)
def _run_config_parser(argv):
per_host_cfg = PerHostConfig("phylo_pipeline")
usage_str = "%prog <command> [options] [makefiles]"
version_str = "%%prog %s" % (pypeline.__version__, )
parser = optparse.OptionParser(usage=usage_str, version=version_str)
parser.formatter = CustomHelpFormatter()
parser.formatter.set_parser(parser)
parser.description = _DESCRIPTION
pypeline.ui.add_optiongroup(parser,
ui_default=PerHostValue("quiet"),
color_default=PerHostValue("on"))
pypeline.logger.add_optiongroup(parser, default=PerHostValue("warning"))
group = optparse.OptionGroup(parser, "Scheduling")
group.add_option(
"--samtools-max-threads",
default=PerHostValue(1),
type=int,
help=
"Maximum number of threads to use when genotyping or building pileups [%default]"
)
group.add_option(
"--examl-max-threads",
default=PerHostValue(1),
type=int,
help=
"Maximum number of threads to use for each instance of ExaML [%default]"
)
group.add_option(
"--max-threads",
default=per_host_cfg.max_threads,
type=int,
help="Maximum number of threads to use in total [%default]")
group.add_option(
"--dry-run",
default=False,
action="store_true",
help=
"If passed, only a dry-run in performed, the dependency tree is printed, "
"and no tasks are executed.")
parser.add_option_group(group)
group = optparse.OptionGroup(parser, "Required paths")
group.add_option(
"--temp-root",
default=per_host_cfg.temp_root,
help="Location for temporary files and folders [%default]")
group.add_option("--samples-root",
default=PerHostValue("./data/samples", is_path=True),
help="Location of BAM files for each sample [%default]")
group.add_option(
"--regions-root",
default=PerHostValue("./data/regions", is_path=True),
help="Location of BED files containing regions of interest [%default]")
group.add_option("--prefix-root",
default=PerHostValue("./data/prefixes", is_path=True),
help="Location of prefixes (FASTAs) [%default]")
group.add_option(
"--refseq-root",
default=PerHostValue("./data/refseqs", is_path=True),
help="Location of reference sequences (FASTAs) [%default]")
group.add_option("--destination",
default="./results",
help="The destination folder for result files [%default]")
parser.add_option_group(group)
group = optparse.OptionGroup(parser, "Files and executables")
group.add_option(
"--list-output-files",
action="store_true",
default=False,
help="List all files generated by pipeline for the makefile(s).")
group.add_option("--list-orphan-files", action = "store_true", default = False,
help = "List all files at destination not generated by the pipeline. " \
"Useful for cleaning up after making changes to a makefile.")
group.add_option("--list-executables",
action="store_true",
default=False,
help="List all executables required by the pipeline, "
"with version requirements (if any).")
parser.add_option_group(group)
return per_host_cfg.parse_args(parser, argv)
def _run_config_parser(argv):
per_host_cfg = PerHostConfig("bam_pipeline")
usage_str = "%prog <command> [options] [makefiles]"
version_str = "%%prog %s" % (pypeline.__version__, )
parser = optparse.OptionParser(usage=usage_str, version=version_str)
parser.add_option("--allow-missing-input-files", action = "store_true", default = False,
help = "Allow processing of lanes, even if the original input files are no-longer " \
"accesible, if for example a network drive is down. This option should be " \
"used with care!")
pypeline.ui.add_optiongroup(parser,
ui_default=PerHostValue("quiet"),
color_default=PerHostValue("on"))
pypeline.logger.add_optiongroup(parser, default=PerHostValue("warning"))
group = optparse.OptionGroup(parser, "Scheduling")
group.add_option(
"--bowtie2-max-threads",
type=int,
default=PerHostValue(1),
help="Maximum number of threads to use per BWA instance [%default]")
group.add_option(
"--bwa-max-threads",
type=int,
default=PerHostValue(1),
help="Maximum number of threads to use per BWA instance [%default]")
group.add_option(
"--max-threads",
type=int,
default=per_host_cfg.max_threads,
help="Maximum number of threads to use in total [%default]")
group.add_option(
"--dry-run",
action="store_true",
default=False,
help="If passed, only a dry-run in performed, the dependency "
"tree is printed, and no tasks are executed.")
parser.add_option_group(group)
group = optparse.OptionGroup(parser, "Required paths")
group.add_option("--jar-root", default = PerHostValue("~/install/jar_root", is_path = True),
help = "Folder containing Picard JARs (http://picard.sf.net), " \
"and GATK (www.broadinstitute.org/gatk). " \
"The latter is only required if realigning is enabled. " \
"[%default]")
group.add_option(
"--temp-root",
default=per_host_cfg.temp_root,
help="Location for temporary files and folders [%default/]")
group.add_option(
"--destination",
default=None,
help=
"The destination folder for result files. By default, files will be "
"placed in the same folder as the makefile which generated it.")
parser.add_option_group(group)
group = optparse.OptionGroup(parser, "Files and executables")
group.add_option(
"--list-output-files",
action="store_true",
default=False,
help="List all files generated by pipeline for the makefile(s).")
group.add_option("--list-orphan-files", action = "store_true", default = False,
help = "List all files at destination not generated by the pipeline. " \
"Useful for cleaning up after making changes to a makefile.")
group.add_option("--list-executables",
action="store_true",
default=False,
help="List all executables required by the pipeline, "
"with version requirements (if any).")
parser.add_option_group(group)
group = optparse.OptionGroup(parser, "Targets")
group.add_option(
"--target",
dest="targets",
action="append",
default=[],
help="Only execute nodes required to build specified target.")
group.add_option("--list-targets", default = None, choices = _TARGETS_BY_NAME,
help = "List all targets at a given resolution (%s)" \
% (", ".join(_TARGETS_BY_NAME),))
parser.add_option_group(group)
group = optparse.OptionGroup(parser, "Misc")
group.add_option(
"--jre-option",
dest="jre_options",
action="append",
default=PerHostValue([]),
help="May be specified one or more times with options to be passed "
"tot the JRE (Jave Runtime Environment); e.g. to change the "
"maximum amount of memory (default is -Xmx4g)")
parser.add_option_group(group)
return per_host_cfg.parse_args(parser, argv)