Hello Joel, The main Galaxy tool shed is back up - thanks for reporting this problem. Greg Von Kuster On Sep 30, 2012, at 5:34 PM, Joel Rosenberg wrote:

It looks like the galaxy toolshed is down.

The migration script is trying to download this:

http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bwa_wrappers&owner=devteam&changeset_revision=ffa8aaa14f7c&webapp=install_manager

But this:

http://toolshed.g2.bx.psu.edu

is down:

502 Bad Gateway nginx/1.1.4

<quote author='joel'>

My cloud galaxy cluster can't boot up after attempting a bitbucket update due to a 502 HTTP error when trying to update the DB. Here's the log:

From: thisisjoel@hotmail.com To: galaxy-user@lists.bx.psu.edu Subject: Errors during database migration after updating galaxy Date: Sun, 30 Sep 2012 21:18:11 +0000

My cloud galaxy cluster can't boot up after attempting a bitbucket update due to a 502 HTTP error when trying to update the DB. Here's the log:

/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,318 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2012-09-30 21:13:18,344 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-09-30 21:13:18,610 At database version 107 galaxy.tool_shed.migrate.check DEBUG 2012-09-30 21:13:18,620 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 47, in __init__ verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/check.py", line 54, in verify_tools missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 33, in check_for_missing_tools response = urllib2.urlopen( url ) File "/usr/lib/python2.6/urllib2.py", line 126, in urlopen return _opener.open(url, data, timeout) File "/usr/lib/python2.6/urllib2.py", line 397, in open response = meth(req, response) File "/usr/lib/python2.6/urllib2.py", line 510, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python2.6/urllib2.py", line 435, in error return self._call_chain(*args) File "/usr/lib/python2.6/urllib2.py", line 369, in _call_chain result = func(*args) File "/usr/lib/python2.6/urllib2.py", line 518, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 502: Bad Gateway Removing PID file paster.pid ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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