# HG changeset patch
# User gga
# Date 1673437521 0
# Node ID 662531e6cfec119a4f6876586b8dfbf7323d4d65
# Parent d96ac610afac34f7106800d436eb73aabbab33b9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
diff -r d96ac610afac -r 662531e6cfec create_or_update_organism.py
--- a/create_or_update_organism.py Fri Dec 10 09:44:10 2021 +0000
+++ b/create_or_update_organism.py Wed Jan 11 11:45:21 2023 +0000
@@ -88,7 +88,7 @@
# Cleanup if existing
if not IsRemote():
- if(os.path.exists(args.jbrowse)):
+ if os.path.exists(args.jbrowse):
shutil.rmtree(args.jbrowse)
# Copy files
shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True)
diff -r d96ac610afac -r 662531e6cfec fetch_organism_jbrowse.xml
--- a/fetch_organism_jbrowse.xml Fri Dec 10 09:44:10 2021 +0000
+++ b/fetch_organism_jbrowse.xml Wed Jan 11 11:45:21 2023 +0000
@@ -4,7 +4,9 @@
macros.xml
-
+
+ rsync
+
= 10:
+ from collections.abc import MutableMapping
+else:
+ from collections import MutableMapping
+
import requests
from six.moves.builtins import next
@@ -29,7 +35,7 @@
# of https://github.com/tkem/cachetools/ #
#############################################
-class DefaultMapping(collections.MutableMapping):
+class DefaultMapping(MutableMapping):
__slots__ = ()
@@ -436,7 +442,6 @@
def __init__(self):
if 'ARROW_GLOBAL_CONFIG_PATH' in os.environ:
-
with open(os.environ['ARROW_GLOBAL_CONFIG_PATH'], 'r') as config:
conf = yaml.safe_load(config)
try: