# HG changeset patch
# User gga
# Date 1673437704 0
# Node ID d91f4bc313d34e6a2f135f5dc32f7fb08b672a1f
# Parent  654af4ba76bcc0f5ecf670d7f63d883b84a4cf8e
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b

diff -r 654af4ba76bc -r d91f4bc313d3 create_or_update_organism.py
--- a/create_or_update_organism.py	Fri Dec 10 09:50:40 2021 +0000
+++ b/create_or_update_organism.py	Wed Jan 11 11:48:24 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 654af4ba76bc -r d91f4bc313d3 fetch_organism_jbrowse.xml
--- a/fetch_organism_jbrowse.xml	Fri Dec 10 09:50:40 2021 +0000
+++ b/fetch_organism_jbrowse.xml	Wed Jan 11 11:48:24 2023 +0000
@@ -4,7 +4,9 @@
   <macros>
     <import>macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
+  <expand macro="requirements">
+    <requirement type="package" version="3.2.7">rsync</requirement>
+  </expand>
   <code file="webapollo.py"/>
   <command detect_errors="aggressive"><![CDATA[
 mkdir -p '$jbrowse.files_path/'
diff -r 654af4ba76bc -r d91f4bc313d3 webapollo.py
--- a/webapollo.py	Fri Dec 10 09:50:40 2021 +0000
+++ b/webapollo.py	Wed Jan 11 11:48:24 2023 +0000
@@ -5,9 +5,15 @@
 import json
 import logging
 import os
+import sys
 import time
 from abc import abstractmethod
 
+if sys.version_info.major == 3 and sys.version_info.minor >= 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: