Hi Hernán, the bitbucket repository has been abandoned and so the code you are using is not maintained any more, please get it with git from https://github.com/galaxyproject/galaxy
More information are on the wiki: https://wiki.galaxyproject.org/Admin/GetGalaxy
Cheers, Nicola
On 27/10/16 18:47, Hernán Piqueras wrote:
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#insecureplatformwarn.... 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#insecureplatformwarn.... 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#insecureplatformwarn.... 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?
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