Also don't copy subdirectories in an analysis directory tree being copied
from elsewhere.
if not 'DJANGO_SETTINGS_MODULE' in os.environ:
os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
if not 'DJANGO_SETTINGS_MODULE' in os.environ:
os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
from htsworkflow.util import api
from htsworkflow.util.rdfhelp import \
dafTermOntology, \
from htsworkflow.util import api
from htsworkflow.util.rdfhelp import \
dafTermOntology, \
logger.warn("File %s doesn't exist.", a)
if opts.make_link_tree_from is not None:
logger.warn("File %s doesn't exist.", a)
if opts.make_link_tree_from is not None:
- results.make_tree_from(opts.make_tree_from, link=True)
+ results.make_tree_from(opts.make_link_tree_from, link=True)
if opts.copy_tree_from is not None:
if opts.copy_tree_from is not None:
- results.make_tree_from(opts.make_tree_from, link=False)
+ results.make_tree_from(opts.copy_tree_from, link=False)
if opts.fastq:
logger.info("Building fastq extraction scripts")
if opts.fastq:
logger.info("Building fastq extraction scripts")
"""
from collections import MutableMapping
import os
"""
from collections import MutableMapping
import os
import logging
from collections import namedtuple
import logging
from collections import namedtuple
if not os.path.exists(source_pathname):
raise IOError(
"{0} does not exist".format(source_pathname))
if not os.path.exists(source_pathname):
raise IOError(
"{0} does not exist".format(source_pathname))
- if not os.path.exists(target_pathname):
+ if not (os.path.exists(target_pathname) or os.path.isdir(source_pathname)):
if link:
os.symlink(source_pathname, target_pathname)
else:
if link:
os.symlink(source_pathname, target_pathname)
else:
- os.copy(source_pathname, target_pathname)
+ shutil.copy(source_pathname, target_pathname)
LOGGER.info(
'LINK {0} to {1}'.format(source_pathname,
target_pathname))
LOGGER.info(
'LINK {0} to {1}'.format(source_pathname,
target_pathname))