lorax was tested under Anaconda Python 3.6. Begin by downloading it and
making sure that it is in your PATH.   

lorax requires some packages that are in non-default channels, which
may be obtained by the following:

	conda config --add channels conda-forge
	conda config --add channels defaults
	conda config --add channels bioconda

After the channels are configured, update the installation by issuing the command:

	conda update --all

This command usually results in several packages being superseded and updated.

Although it is possible to run lorax directly from the main Anaconda installation,
it is not advisable to do so because lorax's dependencies could break other python
packages you may wish to install.  For this reason, it is preferable to create a
python virtual environment where lorax and its dependencies live.
I prefer to use the name "loraxenv" for this 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
following commands:

	conda create -y --name loraxenv biopython click croniter \
           flask freetype gunicorn hmmer msgpack-python raxml redis \
           redis-py itsdangerous jinja2 markupsafe six werkzeug
	source activate loraxenv
	
If you are installing under MacOS (and only under MacOS), gcc and libgcc
MUST be installed in the current virtual environment:

	conda install gcc libgcc

With the current conda version (4.3.21), there are three packages in the default
channels that are too old for use with lorax: setuptools (27.2.0, should be >30.3.0)
markupsafe (0.23, should be 1.0.0),  
and gunicorn (19.1.0, should be 19.7.1).  Updating setuptools in the root installation
has the possible side effect of breaking any further Anaconda installations, which
is why lorax needs to be installed in a virtual environment.  To update these

	pip install -U gunicorn markupsafe
	pip install -U setuptools

The last command produces an error; don't be worried by it.  Now we are ready
 to install lorax itself:

	pip install --global-option=build_py lorax

Now pick up some dependencies that pip may not have installed
properly from requirements.txt:

	pip install git+git://github.com/Supervisor/supervisor.git@2c601db
	pip install superlance setuptools-scm

Next, we define a command of convenience for running a script that
defines two environmental variables and activates the correct virtual
environment from _outside_ the virtual environment:

    alias runinenv="${CONDA_PREFIX}/bin/run_in_lorax_env"
    source deactivate

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