The web server replaces the graphical user interfaces,
which I will no longer maintain.
If you want to run a lot of analyses using SAP you should install the command line tool on your own machine.
Even if you have never used a command line tool before you will be up and running in half an hour.
Once SAP is installed you run can run it on sequences in a fasta file
mydata.fasta like this:
sap --project myanalysis mydata.fasta
and your results will end up in a folder named
To run SAP you need Python (version 2.7 not 3.*) on your machine. If you are on a Mac or Unix/Linux system you already have that. If you are on Windows you need a Python distribution that comes with the mingw package because Python needs this to compile SAP. I recommend the Anaconda distribution from Continuum Analytics. SAP also needs clustalw2 and blast for alignments and database search so you need to install them on your on your machine too.
The latest stable version of the source code is always available on Github where you can download a zipped version of the code. If you have git installed you can clone the proejct this way:
git clone https://github.com/kaspermunch/sap.git
If you downloaded a zipped package you must first unpack it (not open it). Right-click and select unpack.On Mac/Linux open the Terminal application. On Windows right-click on the Cmd application and click "Open as administrator". Then navigate into the unpacked directory containing the file setup.py. If you are unfamiliar with the Cmd on Windows you can look herefor a guide.
On Windows execute the following commands:
python setup.py setopt --command=build --option=compiler --set-value=mingw32 python setup.py install
On Mac/Linux you execute the following command:
sudo python setup.py installIf you prefer pip you can do this instead:
sudo pip install .
Compiling the program issues a lot of warnings. Do not worry about this. If you don't get any error messages at the end you are fine.
If you do not have admin privileges or just want to install in some non-default
some_dir you first make sure the following set of nested directories
some_dir/lib/python2.7/site-packages (if your python is 2.7).
You then just type:
python setup.py install --prefix=<some_dir>Or you can just install in your user directory with pip:
pip install --user .
If you install in a non-default location you need to ensure that the install directory for the scripts is included in your PATH environmental variable and that the package install directory is included in the PYTHONPATH environmental variable . These variables are usually set in your .bachrc or .profile file like this:
On Windows you need to help you operating system find the
sap script by doing