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JAEILs-iMac:galaxy-dev jaeilhan$ sh run.sh |
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Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample |
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Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample |
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Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample |
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Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample |
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Initializing lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml from user_info.xml.sample |
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Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample |
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Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample |
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Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample |
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Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample |
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Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample |
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Initializing tool-data/add_scores.loc from add_scores.loc.sample |
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Initializing tool-data/alignseq.loc from alignseq.loc.sample |
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Initializing tool-data/all_fasta.loc from all_fasta.loc.sample |
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Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample |
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Initializing tool-data/binned_scores.loc from binned_scores.loc.sample |
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Initializing tool-data/codingSnps.loc from codingSnps.loc.sample |
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Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample |
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Initializing tool-data/faseq.loc from faseq.loc.sample |
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Initializing tool-data/funDo.loc from funDo.loc.sample |
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Initializing tool-data/liftOver.loc from liftOver.loc.sample |
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Initializing tool-data/maf_index.loc from maf_index.loc.sample |
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Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample |
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Initializing tool-data/microbial_data.loc from microbial_data.loc.sample |
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Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample |
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Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample |
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Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample |
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Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample |
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Initializing tool-data/phastOdds.loc from phastOdds.loc.sample |
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Initializing tool-data/picard_index.loc from picard_index.loc.sample |
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Initializing tool-data/quality_scores.loc from quality_scores.loc.sample |
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Initializing tool-data/regions.loc from regions.loc.sample |
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Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample |
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Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample |
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Initializing tool-data/sift_db.loc from sift_db.loc.sample |
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Initializing tool-data/srma_index.loc from srma_index.loc.sample |
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Initializing tool-data/twobit.loc from twobit.loc.sample |
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Initializing static/welcome.html from welcome.html.sample |
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Some eggs are out of date, attempting to fetch... |
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Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/repoze.lru/repoze.lru-0.6-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/ordereddict/ordereddict-1.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-2.4.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/lrucache/lrucache-0.2-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.9.6-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/amqp/amqp-1.4.6-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/bx_python/bx_python-0.7.2-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/PasteDeploy/PasteDeploy-1.5.0-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-1.3-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.5.2-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/docutils/docutils-0.7-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.24-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/numpy/numpy-1.6.0-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/mock/mock-1.0.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/PyYAML/PyYAML-3.10-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/SQLAlchemy/SQLAlchemy-1.0.8-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/simplejson/simplejson-2.1.1-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/sqlparse/sqlparse-0.1.14-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/NoseTestDiff/NoseTestDiff-0.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/poster/poster-0.8.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/python_lzo/python_lzo-1.08_2.03_static-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/wchartype/wchartype-0.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Tempita/Tempita-0.5.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/MarkupSafe/MarkupSafe-0.12-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Routes/Routes-2.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/six/six-1.9.0-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/decorator/decorator-3.1.2-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/importlib/importlib-1.0.3-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/WebOb/WebOb-0.8.5-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/pycrypto/pycrypto-2.5-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/Paste/Paste-1.7.5.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/python_daemon/python_daemon-1.5.5-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/mercurial/mercurial-3.2.4-py2.7-macosx-10.6-intel-ucs2.egg |
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Fetched http://eggs.galaxyproject.org/wsgiref/wsgiref-0.1.2-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/pytz/pytz-2013.9-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/nose/nose-1.3.6-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/requests/requests-2.2.1-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/anyjson/anyjson-0.3.3-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/WebError/WebError-0.8a-py2.7.egg |
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Fetched http://eggs.galaxyproject.org/twill/twill-0.9-py2.7.egg |
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Fetch successful. |
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Traceback (most recent call last): |
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File "./scripts/paster.py", line 32, in <module> |
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serve.run() |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1052, in run |
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invoke(command, command_name, options, args[1:]) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1058, in invoke |
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exit_code = runner.run(args) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 221, in run |
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result = self.command() |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 637, in command |
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app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 352, in loadapp |
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return loadobj(APP, uri, name=name, **kw) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 376, in loadobj |
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global_conf=global_conf) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 401, in loadcontext |
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global_conf=global_conf) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 425, in _loadconfig |
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return loader.get_context(object_type, name, global_conf) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 563, in get_context |
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section) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 622, in _context_from_explicit |
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value = import_string(found_expr) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 127, in import_string |
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return pkg_resources.EntryPoint.parse("x=" + s).load(False) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/pkg_resources.py", line 1954, in load |
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entry = __import__(self.module_name, globals(),globals(), ['__name__']) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/web/buildapp.py", line 5, in <module> |
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from galaxy.webapps.galaxy.buildapp import app_factory |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module> |
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import galaxy.app |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/app.py", line 9, in <module> |
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import galaxy.queues |
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File "/Users/jaeilhan/Downloads/galaxy-dev/lib/galaxy/queues.py", line 19, in <module> |
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from kombu import Exchange, Queue, Connection |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/__init__.py", line 67, in __getattr__ |
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module = __import__(object_origins[name], None, None, [name]) |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/entity.py", line 10, in <module> |
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from .abstract import MaybeChannelBound |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/abstract.py", line 12, in <module> |
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from .connection import maybe_channel |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/connection.py", line 19, in <module> |
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from kombu import exceptions |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/exceptions.py", line 12, in <module> |
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from amqp import ChannelError, ConnectionError, ResourceError |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/amqp-1.4.6-py2.7.egg/amqp/__init__.py", line 32, in <module> |
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from .basic_message import Message # noqa |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/amqp-1.4.6-py2.7.egg/amqp/basic_message.py", line 19, in <module> |
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from .serialization import GenericContent |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/amqp-1.4.6-py2.7.egg/amqp/serialization.py", line 33, in <module> |
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from .five import int_types, long_t, string, string_t, items |
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File "/Users/jaeilhan/Downloads/galaxy-dev/eggs/amqp-1.4.6-py2.7.egg/amqp/five.py", line 145, in <module> |
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libSystem = ctypes.CDLL('libSystem.dylib') |
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File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 365, in __init__ |
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self._handle = _dlopen(self._name, mode) |
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OSError: dlopen(libSystem.dylib, 6): image not found |
