On Mon, May 5, 2014 at 2:30 PM, Dannon Baker <[email protected]> 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? > In any event, I'm changing the order of those requires in > 13302:92519a9bfa32, which may resolve your issue. They work fine like that > in production with eggs fetched ahead of time, but I could see how that'd > cause the failure you're seeing. https://bitbucket.org/galaxy/galaxy-central/commits/92519a9bfa32a42ce47a63fdb72c8e2d717ec52e It looks like John has his Galaxy mirror automatically updates (or he did a push just now), so I could ask TravisCI to retest immediately. [In earlier testing GitHub was faster than BitBucket for fetching Galaxy]: https://github.com/jmchilton/galaxy-central/commit/9e72c14ef176e494a611bee6441477a05fb8e677 Unfortunately, no real change: ... functional_tests.py INFO 2014-05-05 13:44:46,611 Embedded Universe application started galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,684 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,685 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,758 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,762 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,765 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,773 Enabling 'tool_runner' controller, class: ToolRunner galaxy.eggs DEBUG 2014-05-05 13:44:46,958 Fetched http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,189 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,190 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,202 Enabling 'data_admin' controller, class: DataAdmin galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,246 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,256 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,260 Enabling 'ucsc_proxy' controller, class: UCSCProxy 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 13:44:47,295 sending stop signal to worker thread galaxy.jobs.handler INFO 2014-05-05 13:44:47,296 job handler queue stopped ... Peter ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
