Hi all,

I've got a relatively fresh installed Galaxy instance running within a locked network, where internet access is allowed only via a proxy. So far, so simple; indeed I get internet access via a terminal (e.g. calling Google with lynx), also wget and mercurial have the chance to access target URL's. The variables $http_proxy, $https_proxy and $ftp_proxy are set.

My problem occurs when I try to execute the automatic tests (using 'run_functional_tests.sh') for the FASTX toolbox, described here right at the end:

The calls of the scripts generally end up in an error block of the following scheme:

functional_tests.py DEBUG 2013-06-25 14:15:40,406 Attempting to serve app on randomly chosen port: 8720
functional_tests.py INFO 2013-06-25 14:15:40,468 Embedded web server started
base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.text
base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.tabular
base.asserts DEBUG 2013-06-25 14:15:40,506 base.asserts.xml
functional_tests.py INFO 2013-06-25 14:15:40,506 Functional tests will be run against localhost:8720 nose.plugins.manager DEBUG 2013-06-25 14:15:40,518 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTes
nose.plugins.manager DEBUG 2013-06-25 14:15:40,520 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML
Uncollapse ( cshl_fastx_uncollapser ) > Test-1 ... ERROR

ERROR: Uncollapse ( cshl_fastx_uncollapser ) > Test-1
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 53, in setUp
File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 1141, in home
    self.visit_url( self.url )
File "/home/galaxy/galaxy-dist/test/base/twilltestcase.py", line 1324, in visit_url
    tc.code( 200 )
File "/home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/commands.py", line 133, in code
TwillAssertionError: code is 403 != 200

Ran 1 test in 0.011s

FAILED (errors=1)

For me it reads like there is problem while testing to call the URL in self.url, which resolves to 'localhost:9441'. URL and port are drawn from the environment in the script ".../galaxy-dist/test/base/twilltestcase.py":

class TwillTestCase( unittest.TestCase ):

    def setUp( self ):
        self.host = os.environ.get( 'GALAXY_TEST_HOST' )
        self.port = os.environ.get( 'GALAXY_TEST_PORT )
        self.url = "http://%s:%s"; % ( self.host, self.port )


I could neither observe any process listening to port 9441 during the test script execution, nor any of the text files within the galaxy root dir contained '9441' as part of a configuration option.

Finally I'm a bit confused what that means to me, beyond just not to be able to use the test suite. Anyone an idea what could and/or should be fixed or checked?

Thanks in advance,


Sebastian Schaaf, M.Sc. Bioinformatics
Department of Medical Informatics,
 Biometry and Epidemiology (IBE)
University of Munich

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