Download and install SAP

If you only want to run a single analysis using SAP you can use the web server. Otherwise you should install SAP on your own machine.

On Mac and Linux, installation is straight forward (see below). If you are on a Windows machine, SAP can be installed through Docker. This also lets you user the webserver interface on your local machine. Feel free to contact me if you are interested in this.

Make a conda environment

The easiest way to install the command line version of SAP on Mac and Linux is to first install Anaconda Python. Once that is done you can create a conda environment. The command for doing this depends on your operating system.

On Linux use this command:

conda create --name sap -c conda-forge -c bioconda -c biobuilds -c anaconda python=2.7 blast clustalw biopython==1.75 gcc_linux-64 git

On Mac use this command:

conda create --name sap -c conda-forge -c bioconda -c biobuilds -c anaconda python=2.7 blast clustalw biopython==1.75 clang_osx-64 git

Activate environment

Activate the `sap` environment like this:

conda activate sap

Download SAP from GitHub

Then clone the SAP source code from GitHub:

git clone https://github.com/kaspermunch/sap.git

Install SAP

Then enter the `sap` directory and install sap:

cd sap

Then install sap:

python setup.py install

That's it.

Run SAP

To run sap you must always first acativate the sap environment where you installed it:

conda activate sap

Then you can run sap. Here just to see the help text:

sap --help

See the documentation for how to use sap on the command line.