Change made:
https://github.com/peterjc/pico_galaxy/commit/19d24c71b5c24cb908907f25e5d992627165736c
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-linux-x86_64-ucs4.egg
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.egg
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-py2.7.egg
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-ucs4.egg
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-linux-x86_64-ucs4.egg
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-ucs4.egg
Fetched 
http://eggs.galaxyproject.org/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg
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-linux-x86_64-ucs4.egg
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-ucs4.egg
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_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.7.egg
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.egg
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-ucs4.egg
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.ba...@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?
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