Guys
I am running CentOS 6.8 in a virtualenv and no matter what, I always
get pkg_resources.DistributionNotFound: Paste
These were the commands to install and launch Galaxy
hg clone https://bitbucket.org/galaxy/galaxy-dist
wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py
<http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py>
/usr/local/bin/python2.7 virtualenv.py --no-site-packages galaxy_env
. ./galaxy_env/bin/activate
source ~/galaxy_env/bin/activate
sh galaxy-dist/run.sh
and even tried to start with some workarounds found in the web (in no
particular order):
cd /home/galaxy/galaxy-dist && ./scripts/common_startup.sh
./scripts/common_startup.sh --skip-venv --dev-wheels
sh galaxy-dist/run.sh --skip-venv --dev-wheels
sh galaxy-dist/run.sh --skip-venv
sh galaxy-dist/run.sh --replace-pip
easy_install paste
Also install or upgrade doesn't solve the problem:
(galaxy_env)bash-4.1$ pip install paste
Requirement already satisfied (use --upgrade to upgrade): paste in
./galaxy_env/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): six in
./galaxy_env/lib/python2.7/site-packages (from paste)
(galaxy_env)bash-4.1$ pip install paste --upgrade
/home/galaxy/galaxy_env/lib/python2.7/site-packages/pip-8.1.2-py2.7.egg/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318:
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. You can upgrade to a
newer version of Python to solve this. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
SNIMissingWarning
/home/galaxy/galaxy_env/lib/python2.7/site-packages/pip-8.1.2-py2.7.egg/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122:
InsecurePlatformWarning: A true SSLContext object is not available.
This prevents urllib3 from configuring SSL appropriately and may cause
certain SSL connections to fail. You can upgrade to a newer version of
Python to solve this. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
InsecurePlatformWarning
Collecting paste
Using cached Paste-2.0.3-py2-none-any.whl
Collecting six>=1.4.0 (from paste)
Using cached six-1.10.0-py2.py3-none-any.whl
Installing collected packages: six, paste
Found existing installation: six 1.9.0
Uninstalling six-1.9.0:
Successfully uninstalled six-1.9.0
Found existing installation: Paste 2.0.2
Uninstalling Paste-2.0.2:
Successfully uninstalled Paste-2.0.2
Successfully installed paste-2.0.3 six-1.10.0
Using common_startup.sh also doesn't solve the problem:
(galaxy_env)bash-4.1$ cd /home/galaxy/galaxy-dist &&
./scripts/common_startup.sh
Activating virtualenv at .venv
Ignoring indexes: https://pypi.python.org/simple
/home/galaxy/galaxy-dist/.venv/lib/python2.7/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
/home/galaxy/galaxy-dist/.venv/lib/python2.7/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#insecureplatformwarning.
InsecurePlatformWarning
Requirement already up-to-date: pip==8.0.2+gx2 in
./.venv/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade):
bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade):
MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 3))
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied (use --upgrade to upgrade):
SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 5))
Requirement already satisfied (use --upgrade to upgrade):
mercurial==3.4.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 7))
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
Requirement already satisfied (use --upgrade to upgrade):
pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 9))
Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
16))
Requirement already satisfied (use --upgrade to upgrade):
PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 17))
Requirement already satisfied (use --upgrade to upgrade):
docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 18))
Requirement already satisfied (use --upgrade to upgrade):
wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 19))
Requirement already satisfied (use --upgrade to upgrade):
repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 20))
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
21))
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
22))
Requirement already satisfied (use --upgrade to upgrade):
WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 23))
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
24))
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
25))
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
26))
Requirement already satisfied (use --upgrade to upgrade):
Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 27))
Requirement already satisfied (use --upgrade to upgrade):
Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 30))
Requirement already satisfied (use --upgrade to upgrade):
Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 31))
Requirement already satisfied (use --upgrade to upgrade):
bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 34))
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
35))
Requirement already satisfied (use --upgrade to upgrade):
requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 36))
Requirement already satisfied (use --upgrade to upgrade):
requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from
-r requirements.txt (line 37))
Requirement already satisfied (use --upgrade to upgrade):
kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 40))
Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
41))
Requirement already satisfied (use --upgrade to upgrade):
anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 42))
Requirement already satisfied (use --upgrade to upgrade):
sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages
(from -r requirements.txt (line 45))
Requirement already satisfied (use --upgrade to upgrade):
decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 46))
Requirement already satisfied (use --upgrade to upgrade):
Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 47))
Requirement already satisfied (use --upgrade to upgrade):
sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 48))
Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
49))
Requirement already satisfied (use --upgrade to upgrade): six==1.9.0
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
51))
Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
52))
Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
53))
Requirement already satisfied (use --upgrade to upgrade):
SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 54))
Requirement already satisfied (use --upgrade to upgrade):
Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 57))
Requirement already satisfied (use --upgrade to upgrade):
paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 58))
Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
59))
Requirement already satisfied (use --upgrade to upgrade):
Whoosh==2.4.1+gx1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 66))
Requirement already satisfied (use --upgrade to upgrade):
pysam==0.8.4+gx1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 69))
You are using pip version 8.0.2+gx2, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Requirement already satisfied (use --upgrade to upgrade): MySQL-python
in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1))
You are using pip version 8.0.2+gx2, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(galaxy_env)bash-4.1$ ./galaxy-dist/scripts/common_startup.sh --skip-venv
Could not open requirements file: [Errno 2] No such file or directory:
'requirements.txt'
This is the complete log (with normal startup):
(galaxy_env)bash-4.1$ sh galaxy-dist/run.sh
Activating virtualenv at .venv
Ignoring indexes: https://pypi.python.org/simple
/home/galaxy/galaxy-dist/.venv/lib/python2.7/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
/home/galaxy/galaxy-dist/.venv/lib/python2.7/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#insecureplatformwarning.
InsecurePlatformWarning
Requirement already up-to-date: pip==8.0.2+gx2 in
./.venv/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade):
bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade):
MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 3))
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied (use --upgrade to upgrade):
SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 5))
Requirement already satisfied (use --upgrade to upgrade):
mercurial==3.4.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 7))
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
Requirement already satisfied (use --upgrade to upgrade):
pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 9))
Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
16))
Requirement already satisfied (use --upgrade to upgrade):
PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 17))
Requirement already satisfied (use --upgrade to upgrade):
docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 18))
Requirement already satisfied (use --upgrade to upgrade):
wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 19))
Requirement already satisfied (use --upgrade to upgrade):
repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 20))
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
21))
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
22))
Requirement already satisfied (use --upgrade to upgrade):
WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 23))
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
24))
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
25))
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
26))
Requirement already satisfied (use --upgrade to upgrade):
Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 27))
Requirement already satisfied (use --upgrade to upgrade):
Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 30))
Requirement already satisfied (use --upgrade to upgrade):
Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 31))
Requirement already satisfied (use --upgrade to upgrade):
bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 34))
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
35))
Requirement already satisfied (use --upgrade to upgrade):
requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 36))
Requirement already satisfied (use --upgrade to upgrade):
requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from
-r requirements.txt (line 37))
Requirement already satisfied (use --upgrade to upgrade):
kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 40))
Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
41))
Requirement already satisfied (use --upgrade to upgrade):
anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 42))
Requirement already satisfied (use --upgrade to upgrade):
sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages
(from -r requirements.txt (line 45))
Requirement already satisfied (use --upgrade to upgrade):
decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 46))
Requirement already satisfied (use --upgrade to upgrade):
Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 47))
Requirement already satisfied (use --upgrade to upgrade):
sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 48))
Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
49))
Requirement already satisfied (use --upgrade to upgrade): six==1.9.0
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
51))
Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
52))
Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
53))
Requirement already satisfied (use --upgrade to upgrade):
SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 54))
Requirement already satisfied (use --upgrade to upgrade):
Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 57))
Requirement already satisfied (use --upgrade to upgrade):
paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 58))
Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line
59))
Requirement already satisfied (use --upgrade to upgrade):
Whoosh==2.4.1+gx1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 66))
Requirement already satisfied (use --upgrade to upgrade):
pysam==0.8.4+gx1 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 69))
You are using pip version 8.0.2+gx2, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Requirement already satisfied (use --upgrade to upgrade): MySQL-python
in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1))
You are using pip version 8.0.2+gx2, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Activating virtualenv at .venv
Traceback (most recent call last):
File "./scripts/paster.py", line 27, in <module>
serve.run()
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
1061, in run
invoke(command, command_name, options, args[1:])
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
1067, in invoke
exit_code = runner.run(args)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
223, in run
result = self.command()
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
637, in command
server = loadserver(server_spec, name=server_name,
relative_to=base, global_conf=vars)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 303, in loadserver
return loadobj(SERVER, uri, name=name, **kw)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 319, in loadobj
global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 344, in loadcontext
global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 368, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 502, in get_context
section)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 524, in _context_from_use
object_type, name=use, global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 454, in get_context
global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 344, in loadcontext
global_conf=global_conf)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 376, in _loadegg
return loader.get_context(object_type, name, global_conf)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 668, in get_context
object_type, name=name)
File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 688, in find_egg_entry_point
pkg_resources.require(self.spec)
File
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 666, in require
File
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 565, in resolve
pkg_resources.DistributionNotFound: Paste
Any hints?
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
