Change made: https://github.com/peterjc/pico_galaxy/commit/19d24c71b5c24cb908907f25e5d992... https://travis-ci.org/peterjc/pico_galaxy/builds/24455410 That worked in one sense: $ python scripts/fetch_eggs.py Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-li... Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg Fetched http://eggs.galaxyproject.org/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.2-py... Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.galaxyproject.org/amqp/amqp-1.4.3-py2.7.egg Fetched http://eggs.galaxyproject.org/bx_python/bx_python-0.7.2-py2.7-linux-x86_64-u... Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-1.3-py2.7.egg Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.12-py2.7.egg Fetched http://eggs.galaxyproject.org/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.galaxyproject.org/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-li... Fetched http://eggs.galaxyproject.org/mock/mock-1.0.1-py2.7.egg Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg Fetched http://eggs.galaxyproject.org/PyYAML/PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.galaxyproject.org/SQLAlchemy/SQLAlchemy-0.7.9-py2.7-linux-x86_64... Fetched http://eggs.galaxyproject.org/simplejson/simplejson-2.1.1-py2.7-linux-x86_64... Fetched http://eggs.galaxyproject.org/NoseTestDiff/NoseTestDiff-0.1-py2.7.egg Fetched http://eggs.galaxyproject.org/poster/poster-0.8.1-py2.7.egg Fetched http://eggs.galaxyproject.org/python_lzo/python_lzo-1.08_2.03_static-py2.7-l... Fetched http://eggs.galaxyproject.org/Tempita/Tempita-0.5.1-py2.7.egg Fetched http://eggs.galaxyproject.org/MarkupSafe/MarkupSafe-0.12-py2.7-linux-x86_64-... Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg Fetched http://eggs.galaxyproject.org/Routes/Routes-1.12.3-py2.7.egg Fetched http://eggs.galaxyproject.org/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.galaxyproject.org/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998... Fetched http://eggs.galaxyproject.org/WebOb/WebOb-0.8.5-py2.7.egg Fetched http://eggs.galaxyproject.org/pycrypto/pycrypto-2.5-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg Fetched http://eggs.galaxyproject.org/python_daemon/python_daemon-1.5.5-py2.7.egg Fetched http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-u... Fetched http://eggs.galaxyproject.org/wsgiref/wsgiref-0.1.2-py2.7.egg Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg Fetched http://eggs.galaxyproject.org/pytz/pytz-2013.9-py2.7.egg Fetched http://eggs.galaxyproject.org/nose/nose-0.11.1-py2.7.egg Fetched http://eggs.galaxyproject.org/requests/requests-2.2.1-py2.7.egg Fetched http://eggs.galaxyproject.org/anyjson/anyjson-0.3.3-py2.7.egg Fetched http://eggs.galaxyproject.org/WebError/WebError-0.8a-py2.7.egg Fetched http://eggs.galaxyproject.org/twill/twill-0.9-py2.7.egg However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg the old error persists. Is there a case-sensitivity issue here (PyYAML versus pyyaml)? ... functional_tests.py INFO 2014-05-05 14:23:11,383 Embedded Universe application started galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,385 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,386 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,432 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,438 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,440 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,489 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,490 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,673 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2014-05-05 14:23:11,676 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,194 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,204 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,208 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,219 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,238 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,252 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,260 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,272 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,272 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,274 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,282 Enabling 'data_admin' controller, class: DataAdmin galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,284 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,293 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,321 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,323 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2014-05-05 14:23:12,323 Enabling 'admin' controller, class: AdminGalaxy Traceback (most recent call last): File "./scripts/functional_tests.py", line 601, in <module> sys.exit( main() ) File "./scripts/functional_tests.py", line 417, in main use_translogger=False, static_enabled=STATIC_ENABLED ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py", line 441, in add_ui_controllers module = import_module( module_name ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module __import__(name) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 18, in <module> eggs.require('pyyaml') File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py", line 412, in require return pkg_resources.working_set.require( req_str ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: pyyaml galaxy.jobs.handler INFO 2014-05-05 14:23:12,343 sending stop signal to worker thread ... Thanks! Peter On Mon, May 5, 2014 at 3:10 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Can you add a `python scripts/fetch_eggs.py` to your travis config just after the stop-daemon? That should parse eggs.ini and fetch all of the eggs.
On Mon, May 5, 2014 at 9:51 AM, Peter Cock wrote:
On Mon, May 5, 2014 at 2:30 PM, Dannon Baker wrote:
Hey Peter,
Just looking at the travis job, it looks like there's not a fetch_eggs step at the start, but rather that it's fetching as they're require()'d. Is that correct?
Yes, https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml does not (currently) attempt to fetch any eggs explicitly - it lets the different bits of Galaxy do this on demand.
Is there a simple command line instruction to tell Galaxy to fetch all the eggs it might want?