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"
common_startup.sh rather than attempting to use sha256sum. Older
versions of coreutils (such as in RHEL 6) did not include the --strict
argument to sha256sum.
that contain a `+` in the version. For these older versions, directly
install the wheel or install from the sdist. Technically 1.4 and later
can install wheels, but in testing, only 1.5+ was able to install them
properly with their scripts.
The new heredoc execute and redirect syntax is Bourne-compatible.
pip --pre is no longer necessary since the Galaxy pip version is no
longer a development version of pip.
management. Drop hard requirement on lzo (doubt anyone other than
usegalaxy.org is using it, but it will be added as a extras option for
bxlab/bx-python for anyone who is).
Fixes#1150
than an editable directly from github.
Also, use `set -e` in scripts/common_startup.sh to fail if anything
fails, rather than chaining a bunch of things with `&&` but not properly
handling failure cases.
John Chilton