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Add the option to copy tree in addition to making a symlink tree from elsewhere.
[htsworkflow.git]
/
encode_submission
/
trackhub.py
diff --git
a/encode_submission/trackhub.py
b/encode_submission/trackhub.py
index 41f76d14f6d552f5a25eb0ee1bc74f9db32e18c6..4fea5cc827eca6ef7aa08c39642e6bd4aa1dac0b 100644
(file)
--- a/
encode_submission/trackhub.py
+++ b/
encode_submission/trackhub.py
@@
-27,7
+27,6
@@
import RDF
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, \
@@
-78,10
+77,10
@@
def main(cmdline=None):
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")