Direct Installation
-------------------

Python Version
--------------
lorax will run under python 3.4 and up.  Testing took place under python 3.5
and 3.6.  Make sure that you select the correct version of python
in creating the virual environment.


Update Using Package Manager
----------------------------
We recommend that you start direct installations by making sure your root
python installation is up-to-date before creating a virtual environment
(which may get updated by pip in a non-maintainable way).  Although it is
possible to run lorax directly from the root installation, it is not advisable
to do so because lorax's dependencies could break other
python packages you may wish to install.


Create a Virtual Environment
----------------------------
lorax requires a more recent version of setuptools than that distributed
with python 3.6 as well as the use of pip.  Both of these may break distro
package manager assumptions, so you will need to either create a working
virtual environment or a root environment in user space.

I prefer to use the name "loraxenv" for the virtual
environment to prevent confusion between package and environment names.
You should create this environment as the user under which you intend the
web server to run, using the python version you wish to use selected
as default, with the following commands:

	python3.6 -m virtualenv loraxenv
	cd loraxenv
	source bin/activate

Install/Update with pip
-----------------------
Next use pip to install dependencies:

	pip install -U setuptools # may produce an error, don't worry
	pip install -U numpy biopython
	pip install --global-option=build_py lorax



Put lorax_env script in alias or on path
----------------------------------------
The lorax_env script is the only executable that you will need to control
lorax and associated process. You should usually not put the entire lorax
bin/ directory into your path, as this may cause binaries from the virtual
environment such as python to be used in contexts where they were not intended
to be used.  The easiest way to do this is with a symlink to a directory
on your path, typically ~/bin:

        ln -s /path/to/loraxenv/bin/lorax_env ~/bin
n/

Deactivate virtual environment
------------------------------
You no longer need to work inside the virtual environment you created.  Leave
the virtual environment with the following command:

    deactivate

Next, follow the instructions in INSTALL.configure+run.txt.
