Installation Guide - biologyguy/RD-MCL GitHub Wiki
Installing Python3
RD-MCL requires Python 3.5 or higher to run. While you can install python directly form python.org, it is highly recommended that you use the Anaconda distribution instead, as it bundles a package manager and virtual environment platform along with the Python interpreter. Installation is usually straightforward, so begin by following the instructions on the main Anaconda download page for your specific operating system.
Getting started with conda
Once installed, you should be able to access the conda program from the command line (make sure you restart your
terminal). It's often a good idea to set up a virtual environment to prevent dependency conflicts, allowing you to
safely experiment with new software without fear of interfering with other key system functionality. While completely
optional, if you do decide to create a dedicated environment for BuddySuite you can set it up as follows
(on a Unix system):
$: conda create -n rdmcl python=3.6
$: source activate rdmcl
When you are done with RDMCL for the day, you can easily go back to your original environment:
$: source deactivate
Installing on Linux or Mac OS X
Quirks on Linux
If running a Debian/Ubuntu-based linux distribution, ensure python-dev is installed:
$: sudo apt-get install python-dev
It is also important that you have a C++ compiler installed.
$: sudo apt-get install build-essential
Quirks on Mac
If you are relatively new to scientific computing and are working on a Mac, you will probably need to install the OS X developer tools called 'XCode'. There is a step-by-step guide here.
The rest is the same on Mac or Linux
Assuming you have set up Anaconda, use the program 'pip' to download/install RD-MCL and all its dependencies
$: pip install rdmcl
Then run the rdmcl setup script, which will check for and install a number of dependencies:
$: rdmcl -setup
Now RD-MCL should run from your command line! Try it out:
$: rdmcl -h
Installing from GitHub
Alternatively, you can clone or fork the git repository and run the setup.py script manually. You may need to install dependencies individually if going this route; pay attention to any error messages thrown by setup.py, and use pip or conda to install the problem packages.
$: git clone https://github.com/biologyguy/RD-MCL.git
$: cd RD-MCL
$: python3 setup.py install clean
$: rdmcl -setup
Dependencies
The more complicated dependencies will be installed for you when you run the setup command. These include PSI-PRED and HMMER3. Please note that RD-MCL requires a patched version of a program contained within the HMMER3 package that is not built/installed by any of the standard channels you may use to get HMMER3. You MUST run the RD-MCL setup script if you want to build this program, and you NEED this program to run RD-MCL... So please run the setup script!
The other major non-python dependency required by RD-MCL is a multiple sequence alignment program supported by AlignBuddy. The default and recommended program is Clustal-Omega, which is easily installed using Conda:
$: conda install clustalo
Here is a list of the python packages required by RD-MCL (all are installable through pip):