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Add option to copy source files for a submission.
[htsworkflow.git]
/
htsworkflow
/
submission
/
results.py
diff --git
a/htsworkflow/submission/results.py
b/htsworkflow/submission/results.py
index 36c2c78e7b2b0aac0613217ec2171f84a3c727ba..50077523aca3970a517973adbd69f119f4f17e3d 100644
(file)
--- a/
htsworkflow/submission/results.py
+++ b/
htsworkflow/submission/results.py
@@
-45,7
+45,7
@@
class ResultMap(MutableMapping):
lib_path = os.path.join(basepath, lib_path)
self[lib_id] = lib_path
lib_path = os.path.join(basepath, lib_path)
self[lib_id] = lib_path
- def make_tree_from(self, source_path, destpath = None):
+ def make_tree_from(self, source_path, destpath = None
, link=True
):
"""Create a tree using data files from source path.
"""
if destpath is None:
"""Create a tree using data files from source path.
"""
if destpath is None:
@@
-76,7
+76,10
@@
class ResultMap(MutableMapping):
raise IOError(
"{0} does not exist".format(source_pathname))
if not os.path.exists(target_pathname):
raise IOError(
"{0} does not exist".format(source_pathname))
if not os.path.exists(target_pathname):
- os.symlink(source_pathname, target_pathname)
+ if link:
+ os.symlink(source_pathname, target_pathname)
+ else:
+ os.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))