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Update common_startup.sh to require python2.7 in .venv #2756

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merged 1 commit into from Aug 9, 2016

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commented Aug 9, 2016

by changing the .venv creation to 'virtualenv -p python2.7' we force the python version we need.

The current suggestion on getgalaxy is: https://wiki.galaxyproject.org/Admin/Python
% mkdir ~/galaxy-python
% ln -s /path/to/python2.7 /galaxy-python/python
% export PATH=
/galaxy-python:$PATH

Which break lots of things, since we are working in a virtual environment anyway we can build it from the start with the version we want.

This will require that python 2.7 used in the virtual environment, and prevent breakage from multi-python deployed hosts. This simple change makes the software more accessible.

This edit built fine on OS X 10.10.5
python installed: 2.6, 2.7, 3.2, 3.5

galaxy.queue_worker INFO 2016-08-08 22:14:15,624 Binding and starting galaxy control worker for main
Starting server in PID 69210.
serving on http://127.0.0.1:8080
/Users/benc/Code/github/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does not support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
'storage.' % (dialect.name, dialect.driver))
127.0.0.1 - - [08/Aug/2016:22:39:18 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/52.0.2743.116 Safari/537.36"

Update common_startup.sh to require python2.7 in .venv
by changing the .venv creation to 'virtualenv -p python2.7' we force the python version we need.

The current suggestion on getgalaxy is: https://wiki.galaxyproject.org/Admin/Python
% mkdir ~/galaxy-python
% ln -s /path/to/python2.7 ~/galaxy-python/python
% export PATH=~/galaxy-python:$PATH

Which break lots of things, since we are working in a virtual environment anyway we can build it from the start with the version we want.

This will require that python 2.7 used in the virtual environment, and prevent breakage from multi-python deployed hosts. This simple change makes the software more accessible.

This edit built fine on OS X  10.10.5
python installed: 2.6, 2.7, 3.2, 3.5

galaxy.queue_worker INFO 2016-08-08 22:14:15,624 Binding and starting galaxy control worker for main
Starting server in PID 69210.
serving on http://127.0.0.1:8080
/Users/benc/Code/github/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
  'storage.' % (dialect.name, dialect.driver))
127.0.0.1 - - [08/Aug/2016:22:39:18 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/52.0.2743.116 Safari/537.36"
@martenson

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commented Aug 9, 2016

@galaxybot test this

@mvdbeek

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commented Aug 9, 2016

LGTM, I think that's a nice improvement.

@dannon

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commented Aug 9, 2016

+1, good idea!

@dannon dannon merged commit 77b7e65 into galaxyproject:release_16.07 Aug 9, 2016

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@mvdbeek

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commented Aug 9, 2016

Thanks a lot @BenjaminHCCarr !

@BenjaminHCCarr BenjaminHCCarr deleted the BenjaminHCCarr:patch-2 branch Jul 20, 2017

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