Hi Iry The last but one line: "socket.error: [Errno 98] Address already in use" holds probably the clue. Looks like something else is running on the same port or you didn't stop the reports server before restarting it (after the upgrade) Regards, Hans On 08/17/2012 11:08 PM, Iry Witham wrote:

Hi Team,

Since I upgraded to the latest galaxy-dist I can no longer get the reports interface to function. When I go to galaxy:9001 I get the following server error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). The reports_webapp.log is as follows:

python path is: /hpcdata/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages galaxy.model.custom_types DEBUG 2012-08-07 17:13:53,219 psycopg2 egg successfully loaded for postgres dialect galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,792 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,815 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,909 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,922 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,942 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,947 Enabling 'root' controller, class: Report galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,950 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,971 Enabling 'recursive' middleware /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,708 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,749 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,750 Enabling 'config' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,888 Enabling 'x-forwarded-host' middleware Starting server in PID 6345. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 303, in command serve() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 287, in serve server(app) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1114, in __init__ RequestHandlerClass, ssl_context) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 400, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use Removing PID file reports_webapp.pid

The following is the report_wsgi.ini:

# ---- HTTP Server ----------------------------------------------------------

[server:main]

use = egg:Paste#http port = 9001 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10

# ---- Galaxy Webapps Report Interface -------------------------------------------------

[app:main]

# Specifies the factory for the universe WSGI application paste.app_factory = galaxy.webapps.reports.buildapp:app_factory log_level = DEBUG

# Database connection #database_file = database/universe.sqlite # You may use a SQLAlchemy connection string to specify an external database instead # database_connection = postgres:///galaxy_test?user=postgres&password=postgres database_connection = postgres:///galaxy_1?user=galaxy&password=galaxy

# Where dataset files are saved file_path = database/files # Temporary storage for additional datasets, this should be shared through the cluster new_file_path = database/tmp

# Session support (beaker) use_beaker_session = True session_type = memory session_data_dir = %(here)s/database/beaker_sessions session_key = galaxysessions session_secret = changethisinproduction

# Configuration for debugging middleware # debug = true use_lint = false

# NEVER enable this on a public site (even test or QA) # use_interactive = true

# path to sendmail #sendmail_path = /usr/sbin/sendmail

# Address to join mailing list #mailing_join_addr = galaxy-user-join@bx.psu.edu

# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) ## use_heartbeat = True

# Profiling middleware (cProfile based) ## use_profile = True

# Mail smtp_server = smtp.jax.org error_email_to = cbr-help@jax.org

# Use the new iframe / javascript based layout use_new_layout = true

# Serving static files (needed if running standalone) static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue

I am sure I have something misconfigured, but can't seem to figure it out.

Thanks for the assistance.

Iry

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/