<commit_before>Millstone
==================

Millstone is a distributed bioinformatics software platform designed to facilitate genome engineering for synthetic biology. Automate iterative design, analysis, and debugging for projects involving hundreds of microbial genomes.

## Dependencies

* Postgresql 9.3 (only this version has been tested)
* Unafold (http://dinamelt.rit.albany.edu/download.php)
* Python deps: See requirements.txt / instructions below
* unafold, specifically hybrid-ss-min (http://dinamelt.rit.albany.edu/download.php)


### No longer required (but need to confirm)

* R (for Picard)

## Installation

### Python environment

We recommend using [virtualenv](http://pypi.python.org/pypi/virtualenv) for
creating and managing a sandbox python environment. This strategy makes it easy
to stay up with requirements. Our requirements are listed in `requirements.txt`.
Follow the instructions below to setup your virtualenv and install the required
packages.

#### Setting up a virtual python environment

1. Install [virtualenv](http://www.virtualenv.org/en/latest/index.html) if you don't have it yet. (You may want to install [pip](http://pypi.python.org/pypi/pip/) first.)

2. Create a new virtual environment for this project. This virtual environment isn't part of the project so just put it somewhere on your machine.  I keep all of my virtual environments in the directory ~/pyenvs/.

        $ virtualenv ~/pyenvs/genome-designer-env

    If you want to use a version of python different from the OS default you can specify the python binary with the '-p' option:

        $ virtualenv -p /usr/local/bin/python2.7 ~/pyenvs/genome-designer-env

3. Activate the environment in the shell. This will use `python` and other binaries like `pip` that are located your pyenv. You should do this whenever running any python/django scripts.

        $ source ~/pyenvs/genome-designer-env/bin/activate .

4. Install the dependencies in your virtual environment. We use the convention of running `pip freeze` to a .txt file containing a list of requirements.
Most users will want to do:
<commit_msg>Revert "Update README.md | note about hybrid-ss-min req"<commit_after>Millstone
==================

Millstone is a distributed bioinformatics software platform designed to facilitate genome engineering for synthetic biology. Automate iterative design, analysis, and debugging for projects involving hundreds of microbial genomes.

## Dependencies

* Postgresql 9.3 (only this version has been tested)
* R (for Picard)
* Unafold (http://dinamelt.rit.albany.edu/download.php)
* Python deps: See requirements.txt / instructions below

## Installation

### Python environment

We recommend using [virtualenv](http://pypi.python.org/pypi/virtualenv) for
creating and managing a sandbox python environment. This strategy makes it easy
to stay up with requirements. Our requirements are listed in `requirements.txt`.
Follow the instructions below to setup your virtualenv and install the required
packages.

#### Setting up a virtual python environment

1. Install [virtualenv](http://www.virtualenv.org/en/latest/index.html) if you don't have it yet. (You may want to install [pip](http://pypi.python.org/pypi/pip/) first.)

2. Create a new virtual environment for this project. This virtual environment isn't part of the project so just put it somewhere on your machine.  I keep all of my virtual environments in the directory ~/pyenvs/.

        $ virtualenv ~/pyenvs/genome-designer-env

    If you want to use a version of python different from the OS default you can specify the python binary with the '-p' option:

        $ virtualenv -p /usr/local/bin/python2.7 ~/pyenvs/genome-designer-env

3. Activate the environment in the shell. This will use `python` and other binaries like `pip` that are located your pyenv. You should do this whenever running any python/django scripts.

        $ source ~/pyenvs/genome-designer-env/bin/activate .

4. Install the dependencies in your virtual environment. We use the convention of running `pip freeze` to a .txt file containing a list of requirements.
Most users will want to do:

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