New subject: Question: Cannot start local Galaxy after upgrade to v16.01

19 Apr 2016


      Hi Galaxy Devs,
I posted this question on biostars but didn't get an answer so I'll try
here:
I just tried upgrading my local instance of Galaxy from 15.10 to 16.01.
When I start it up I get an error. Does anyone have any suggestions?
galaxy@galaxy galaxy$ sh run.sh
Activating virtualenv at .venv
DEPRECATION: Python 2.6 is no longer supported by the Python core
team, please upgrade your Python. A future version of pip will drop
support for Python 2.6
Ignoring indexes: https://pypi.python.org/simple
/opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315:
SNIMissingWarning: An HTTPS request has been made, but the SNI
(Subject Name Indication) extension to TLS is not available on this
platform. This may cause the server to present an incorrect TLS
certificate, which can cause validation failures. For more
information, see
https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
  SNIMissingWarning
/opt/galaxy/.venv/lib/python2.6/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120:
InsecurePlatformWarning: A true SSLContext object is not available.
This prevents urllib3 from configuring SSL appropriately and may cause
certain SSL connections to fail. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarn....
  InsecurePlatformWarning
Requirement already up-to-date: pip==8.0.2+gx2 in
./.venv/lib/python2.6/site-packages
DEPRECATION: Python 2.6 is no longer supported by the Python core
team, please upgrade your Python. A future version of pip will drop
support for Python 2.6
Requirement already satisfied (use --upgrade to upgrade):
bx-python==0.7.3 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade):
MarkupSafe==0.23 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 3))
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
4))
Requirement already satisfied (use --upgrade to upgrade):
SQLAlchemy==1.0.8 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 5))
Requirement already satisfied (use --upgrade to upgrade):
mercurial==3.4.2 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 7))
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
8))
Requirement already satisfied (use --upgrade to upgrade):
pycrypto==2.6.1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 9))
Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
16))
Requirement already satisfied (use --upgrade to upgrade):
PasteDeploy==1.5.2 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 17))
Requirement already satisfied (use --upgrade to upgrade):
docutils==0.12 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 18))
Requirement already satisfied (use --upgrade to upgrade):
wchartype==0.1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 19))
Requirement already satisfied (use --upgrade to upgrade):
repoze.lru==0.6 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 20))
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
21))
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
22))
Requirement already satisfied (use --upgrade to upgrade):
WebHelpers==1.3 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 23))
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
24))
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
25))
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
26))
Requirement already satisfied (use --upgrade to upgrade):
Beaker==1.7.0 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 27))
Requirement already satisfied (use --upgrade to upgrade):
Cheetah==2.4.4 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 30))
Requirement already satisfied (use --upgrade to upgrade):
Markdown==2.6.3 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 31))
Requirement already satisfied (use --upgrade to upgrade):
bioblend==0.6.1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 34))
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
35))
Requirement already satisfied (use --upgrade to upgrade):
requests==2.8.1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 36))
Requirement already satisfied (use --upgrade to upgrade):
requests-toolbelt==0.4.0 in ./.venv/lib/python2.6/site-packages (from
-r requirements.txt (line 37))
Requirement already satisfied (use --upgrade to upgrade):
kombu==3.0.30 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 40))
Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
41))
Requirement already satisfied (use --upgrade to upgrade):
anyjson==0.3.3 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 42))
Requirement already satisfied (use --upgrade to upgrade):
sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.6/site-packages
(from -r requirements.txt (line 45))
Requirement already satisfied (use --upgrade to upgrade):
decorator==4.0.2 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 46))
Requirement already satisfied (use --upgrade to upgrade):
Tempita==0.5.3dev in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 47))
Requirement already satisfied (use --upgrade to upgrade):
sqlparse==0.1.16 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 48))
Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
49))
Requirement already satisfied (use --upgrade to upgrade): six==1.9.0
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
51))
Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
52))
Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
53))
Requirement already satisfied (use --upgrade to upgrade):
SVGFig==1.1.6 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 54))
Requirement already satisfied (use --upgrade to upgrade):
Fabric==1.10.2 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 57))
Requirement already satisfied (use --upgrade to upgrade):
paramiko==1.15.2 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 58))
Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13
in ./.venv/lib/python2.6/site-packages (from -r requirements.txt (line
59))
Requirement already satisfied (use --upgrade to upgrade):
Whoosh==2.4.1+gx1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 66))
Requirement already satisfied (use --upgrade to upgrade):
pysam==0.8.4+gx1 in ./.venv/lib/python2.6/site-packages (from -r
requirements.txt (line 69))
Requirement already satisfied (use --upgrade to upgrade): importlib in
./.venv/lib/python2.6/site-packages (from kombu==3.0.30->-r
requirements.txt (line 40))
Requirement already satisfied (use --upgrade to upgrade): ordereddict
in ./.venv/lib/python2.6/site-packages (from kombu==3.0.30->-r
requirements.txt (line 40))
You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
DEPRECATION: Python 2.6 is no longer supported by the Python core
team, please upgrade your Python. A future version of pip will drop
support for Python 2.6
Requirement already satisfied (use --upgrade to upgrade):
psycopg2==2.6.1 in ./.venv/lib/python2.6/site-packages (from -r
/dev/stdin (line 1))
Requirement already satisfied (use --upgrade to upgrade):
importlib==1.0.3 in ./.venv/lib/python2.6/site-packages (from -r
/dev/stdin (line 2))
Requirement already satisfied (use --upgrade to upgrade):
ordereddict==1.1 in ./.venv/lib/python2.6/site-packages (from -r
/dev/stdin (line 3))
Requirement already satisfied (use --upgrade to upgrade): drmaa in
./.venv/lib/python2.6/site-packages (from -r /dev/stdin (line 4))
You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Unsetting $PYTHONPATH
Activating virtualenv at .venv
Traceback (most recent call last):
  File "./scripts/paster.py", line 27, in <module>
    serve.run()
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in run
    invoke(command, command_name, options, args[1:])
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke
    exit_code = runner.run(args)
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 223, in run
    result = self.command()
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 637, in command
    server = loadserver(server_spec, name=server_name,
relative_to=base, global_conf=vars)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
303, in loadserver
    return loadobj(SERVER, uri, name=name, **kw)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
319, in loadobj
    global_conf=global_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
344, in loadcontext
    global_conf=global_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
368, in _loadconfig
    return loader.get_context(object_type, name, global_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
502, in get_context
    section)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
524, in _context_from_use
    object_type, name=use, global_conf=global_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
454, in get_context
    global_conf=global_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
344, in loadcontext
    global_conf=global_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
376, in _loadegg
    return loader.get_context(object_type, name, global_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
668, in get_context
    object_type, name=name)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
688, in find_egg_entry_point
    pkg_resources.require(self.spec)
  File "/opt/galaxy/lib/pkg_resources.py", line 666, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/opt/galaxy/lib/pkg_resources.py", line 565, in resolve
    raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: Paste