X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=blobdiff_plain;f=htsworkflow%2Fsubmission%2Fresults.py;fp=htsworkflow%2Fsubmission%2Fresults.py;h=50077523aca3970a517973adbd69f119f4f17e3d;hp=36c2c78e7b2b0aac0613217ec2171f84a3c727ba;hb=beb3cd40fd1446357399f755f6188968b55fb2df;hpb=d4f592d5c162b136cdf38a5626cea97b9e7844df

diff --git a/htsworkflow/submission/results.py b/htsworkflow/submission/results.py
index 36c2c78..5007752 100644
--- 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
 
-    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:
@@ -76,7 +76,10 @@ class ResultMap(MutableMapping):
                     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))