Re: [galaxy-dev] Cannot start Galaxy DistributionNotFound: Paste

2016-10-27 Thread Nicola Soranzo 

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 



/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

[galaxy-dev] Cannot start Galaxy DistributionNotFound: Paste

2016-10-27 Thread Hernán Piqueras 

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

/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