Mercurial > repos > gga > apollo_fetch_jbrowse
changeset 20:662531e6cfec draft default tip
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
| author | gga |
|---|---|
| date | Wed, 11 Jan 2023 11:45:21 +0000 |
| parents | d96ac610afac |
| children | |
| files | create_or_update_organism.py fetch_organism_jbrowse.xml webapollo.py |
| diffstat | 3 files changed, 11 insertions(+), 4 deletions(-) [+] |
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--- 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)
--- 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> <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/'
--- a/webapollo.py Fri Dec 10 09:44:10 2021 +0000 +++ b/webapollo.py Wed Jan 11 11:45:21 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: