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: thisisj...@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
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