Also don't fail if no config file is found, just print a message on
stderr.
This allows the removal of the code to set `GALAXY_CONFIG_FILE` from
`scripts/common_startup.sh` .
branches), uninstalling psycopg2 will leave psycopg2-binary installed
but in a broken state. If we're removing psycopg2, we need to remove
psycopg2-binary at the same time, leaving psycopg2-binary to be
correctly installed afterwards.
Need to fix https://github.com/galaxyproject/planemo/issues/750 but I don't want to send along command-line arguments that will break older Galaxies, better just to set an environment variable that will be ignored for older Galaxies I think.
Introduced in commit 45a25a1b8b .
This was causing this error on the `dev` branch on Ubuntu (which uses
`dash`):
```
$ ./run.sh
./scripts/common_startup.sh: 69: [: dev: unexpected operator
Activating virtualenv at .venv
...
```
instead of exiting with the "The Galaxy client build is out of date." message.
from PyPI even when a package exists (but the correct version or
architecture does not exist) on wheels.galaxyproject.org. Previously,
PyPI was only checked after wheels.galaxyproject.org because pypiserver
performs an automatic redirect to PyPI for any packages that do not
exist in its index.
So deployers may modify these paths and stil use the default datatypes config.
This should speed up set_metadata also since each of these config files won't be loaded as part of that.
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"
Dannon Baker