def run(config, makefiles):
check_path(config.temp_root)
logfile_template = time.strftime("epiPALEOMIX_pipe.%"
"Y%m%d_%H%M%S_%%02i.log")
pypeline.logger.initialize(config, logfile_template)
logger = logging.getLogger(__name__)
pipeline = Pypeline(config=config)
topnodes = create_nodes(config, makefiles)
assert topnodes, "No analyses to run. Check %s" % (makefiles)
pipeline.add_nodes(topnodes)
if config.list_output_files:
logger.info("Printing output files ...")
pipeline.print_output_files()
return 0
elif config.list_executables:
logger.info("Printing required executables ...")
pipeline.print_required_executables()
return 0
logger.info("Running Epipaleomix pipeline ...")
if not pipeline.run(dry_run=config.dry_run,
max_running=config.max_threads,
progress_ui=config.progress_ui):
return 1
return 0
try:
makefiles = read_makefiles(config, args, commands)
except (MakefileError, pypeline.yaml.YAMLError, IOError), error:
print_err("Error reading makefiles:",
"\n %s:\n " % (error.__class__.__name__,),
"\n ".join(str(error).split("\n")),
file=sys.stderr)
return 1
logfile_template = time.strftime("phylo_pipeline.%Y%m%d_%H%M%S_%%02i.log")
pypeline.logger.initialize(config, logfile_template)
logger = logging.getLogger(__name__)
for (command_key, command_func) in commands:
logger.info("Building %s pipeline ...", command_key)
command_func(pipeline, config, makefiles)
for makefile in makefiles:
if "Nodes" in makefile:
pipeline.add_nodes(makefile["Nodes"])
if config.list_output_files:
logger.info("Printing output files ...")
pipeline.print_output_files()
return 0
elif config.list_orphan_files:
logger.info("Printing orphan files ...")
for filename in sorted(list_orphan_files(config, makefiles, pipeline)):
print(filename)
return 0
"Error reading makefiles:",
"\n %s:\n " % (error.__class__.__name__,),
"\n ".join(str(error).split("\n")),
file=sys.stderr,
)
return 1
logfile_template = time.strftime("bam_pipeline.%Y%m%d_%H%M%S_%%02i.log")
pypeline.logger.initialize(config, logfile_template)
logger = logging.getLogger(__name__)
# Build .fai files for reference .fasta files
index_references(config, makefiles)
if config.list_targets:
logger.info("Listing targets for %s ...", config.list_targets)
for makefile in makefiles:
# If a destination is not specified, save results in same folder as
# the makefile
filename = makefile["Statistics"]["Filename"]
old_destination = config.destination
if old_destination is None:
config.destination = os.path.dirname(filename)
list_targets_for(config, makefile, config.list_targets)
config.destination = old_destination
return 0
pipeline_func = build_pipeline_trimming
if config.targets:
pipeline_func = build_pipeline_targets
try:
makefiles = read_makefiles(config, args, commands)
except (MakefileError, pypeline.yaml.YAMLError, IOError), error:
print_err("Error reading makefiles:",
"\n %s:\n " % (error.__class__.__name__, ),
"\n ".join(str(error).split("\n")),
file=sys.stderr)
return 1
logfile_template = time.strftime("phylo_pipeline.%Y%m%d_%H%M%S_%%02i.log")
pypeline.logger.initialize(config, logfile_template)
logger = logging.getLogger(__name__)
pipeline = Pypeline(config)
for (command_key, command_func) in commands:
logger.info("Building %s pipeline ...", command_key)
command_func(pipeline, config, makefiles)
for makefile in makefiles:
if "Nodes" in makefile:
pipeline.add_nodes(makefile["Nodes"])
if config.list_output_files:
logger.info("Printing output files ...")
pipeline.print_output_files()
return 0
elif config.list_orphan_files:
logger.info("Printing orphan files ...")
for filename in sorted(list_orphan_files(config, makefiles, pipeline)):
print(filename)
return 0
try:
makefiles = read_makefiles(config, args, commands)
except (MakefileError, pypeline.yaml.YAMLError, IOError), error:
print_err("Error reading makefiles:",
"\n %s:\n " % (error.__class__.__name__, ),
"\n ".join(str(error).split("\n")),
file=sys.stderr)
return 1
logfile_template = time.strftime("phylo_pipeline.%Y%m%d_%H%M%S_%%02i.log")
pypeline.logger.initialize(config, logfile_template)
logger = logging.getLogger(__name__)
for (command_key, command_func) in commands:
logger.info("Building %s pipeline ...", command_key)
command_func(pipeline, config, makefiles)
for makefile in makefiles:
if "Nodes" in makefile:
pipeline.add_nodes(makefile["Nodes"])
if config.list_output_files:
logger.info("Printing output files ...")
pipeline.print_output_files()
return 0
elif config.list_orphan_files:
logger.info("Printing orphan files ...")
for filename in sorted(list_orphan_files(config, makefiles, pipeline)):
print(filename)
return 0
except (MakefileError, pypeline.yaml.YAMLError, IOError), error:
print_err("Error reading makefiles:",
"\n %s:\n " % (error.__class__.__name__,),
"\n ".join(str(error).split("\n")),
file=sys.stderr)
return 1
logfile_template = time.strftime("bam_pipeline.%Y%m%d_%H%M%S_%%02i.log")
pypeline.logger.initialize(config, logfile_template)
logger = logging.getLogger(__name__)
# Build .fai files for reference .fasta files
index_references(config, makefiles)
if config.list_targets:
logger.info("Listing targets for %s ...", config.list_targets)
for makefile in makefiles:
# If a destination is not specified, save results in same folder as
# the makefile
filename = makefile["Statistics"]["Filename"]
old_destination = config.destination
if old_destination is None:
config.destination = os.path.dirname(filename)
list_targets_for(config, makefile, config.list_targets)
config.destination = old_destination
return 0
pipeline_func = build_pipeline_trimming
if config.targets:
pipeline_func = build_pipeline_targets
except (MakefileError, pypeline.yaml.YAMLError, IOError), error:
print_err("Error reading makefiles:",
"\n %s:\n " % (error.__class__.__name__, ),
"\n ".join(str(error).split("\n")),
file=sys.stderr)
return 1
logfile_template = time.strftime("bam_pipeline.%Y%m%d_%H%M%S_%%02i.log")
pypeline.logger.initialize(config, logfile_template)
logger = logging.getLogger(__name__)
# Build .fai files for reference .fasta files
index_references(config, makefiles)
if config.list_targets:
logger.info("Listing targets for %s ...", config.list_targets)
for makefile in makefiles:
# If a destination is not specified, save results in same folder as
# the makefile
filename = makefile["Statistics"]["Filename"]
old_destination = config.destination
if old_destination is None:
config.destination = os.path.dirname(filename)
list_targets_for(config, makefile, config.list_targets)
config.destination = old_destination
return 0
pipeline_func = build_pipeline_trimming
if config.targets:
pipeline_func = build_pipeline_targets
try:
makefiles = read_makefiles(config, args, commands)
except (MakefileError, pypeline.yaml.YAMLError, IOError), error:
print_err("Error reading makefiles:",
"\n %s:\n " % (error.__class__.__name__,),
"\n ".join(str(error).split("\n")),
file=sys.stderr)
return 1
logfile_template = time.strftime("phylo_pipeline.%Y%m%d_%H%M%S_%%02i.log")
pypeline.logger.initialize(config, logfile_template)
logger = logging.getLogger(__name__)
pipeline = Pypeline(config)
for (command_key, command_func) in commands:
logger.info("Building %s pipeline ...", command_key)
command_func(pipeline, config, makefiles)
for makefile in makefiles:
if "Nodes" in makefile:
pipeline.add_nodes(makefile["Nodes"])
if config.list_output_files:
logger.info("Printing output files ...")
pipeline.print_output_files()
return 0
elif config.list_orphan_files:
logger.info("Printing orphan files ...")
for filename in sorted(list_orphan_files(config, makefiles, pipeline)):
print(filename)
return 0
