Installing SSTMap
06 Jun 2017The main requirement for installation of SSTMap
is the anaconda python distribution. If you are not familiar with Anaconda, please have a look at continuum.io/why-anaconda. SSTMap is implemented in python 2.7, so if you do not have the anaconda installation, downlaod the anaconda for python 2.7, as shown below. Alternatively, if you have a an anaconda installation for python 3.6, you can create a python 2.7 enviornment to run sstmap.
For instructions on how to download and install Anaconda, please go to Anaconda Download page. The installation is very easy and can be done with the following two steps.
For Linux-64
wget https://repo.continuum.io/archive/Anaconda2-4.3.1-Linux-x86_64.sh
bash Anaconda2-4.3.1-Linux-x86_64.sh
For MacOSX
curl -O https://repo.continuum.io/archive/Anaconda2-4.3.1-MacOSX-x86_64.sh
bash Anaconda2-4.3.1-MacOSX-x86_64.sh
If you already have an anaconda installation for python 3.6, you can install and run SSTMap in a seprate python 2.7 envioronment. The enviornment is created as follows:
conda create -n py27 python=2.7
source activate py27
Conda Installation
The anaconda python distribution comes with conda
package manager, which can then be used to install SSTMap
with the following commands.
conda install sstmap -c omnia -c solvationtools
GitHub Source Code
You can install the latest development version from the GitHub repository by executing
pip install git+git://github.com/kurtzmanlab/sstmap.git@v1.0#egg=sstmap
You can also download the release package manually from GitHub, unzip it, navigate into the directory, and execute the command:
https://github.com/KurtzmanLab/SSTMap/archive/v1.0.tar.gz or https://github.com/KurtzmanLab/SSTMap/archive/v1.0.zip
tar -xvf v1.0.tar.gz or unzip v1.0.zip
cd SSTMap-1.0
python setup.py install
Or you can clone the GitHub repository, navigate into the directory, and execute the command:
git clone git@github.com:KurtzmanLab/SSTMap.git
cd SSTMap
For the release version:
git checkout tags/v1.0
python setup.py install
For the developmental version:
python setup.py install
When building from the source code or using the release package, make sure that you manually install the dependencies: mdtraj
and parmed
. You can do this by:
conda config --add channels omnia
conda install mdtraj parmed
Or using pip:
pip install ParmEd
pip install mdtraj