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) parser.add_option("--to-dot-file", dest="dot_file", help="Write dependency tree to the specified dot-file.") 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)
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),)) group.add_option("--to-dot-file", dest="dot_file", help="Write dependency tree to the specified dot-file.") 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)