Installation and Quick Start

Installing Python for Windows

In order to use cblaster you will first need to install Python on your computer. Go to python.org/downloads/ and download the latest version of Python (3.8.5 at the time of writing). This will initiate the download of the Python installer (python-x.x.x.exe).

Locate the installer in your downloads folder, run the program and follow the wizard. Make sure you tick the box ‘Add Python x.x to PATH’. This ensures that cblaster is available for you to use directly from the terminal. It is not selected by default and you will have to do this step manually if you do not check the box here.

Once the installer has finished, you can try to run Python in PowerShell to verify that it has been installed correctly. To open PowerShell in Windows, open a folder, Shift+Right click and select the option ‘Open PowerShell window here…’. With PowerShell open, type python and press enter. If python has installed correctly, the interactive shell should be launched, and the version number should be displayed in the console like so:

Python 3.8.5 (default, Jul 20 2020, 17:41:41)
Type "help", "copyright", "credits" or "license" for more information.
>>>

The Python package installer tool, pip is installed alongside Python. This is necessary to install cblaster, so verify that it is installed by typing pip --version in PowerShell as above. This should print the version information as well as the Python version and the location like so:

pip 19.2.3 from c:\...\pip (python 3.8)

Installing DIAMOND

cblaster uses DIAMOND to perform local searches. This can be freely obtained from http://www.diamondsearch.org/index.php. Make sure to download and install DIAMOND prior to installing cblaster.

Installing, uninstalling and updating cblaster

To install cblaster, simply input the command:

pip install cblaster

This will install cblaster as well as all of its dependencies.

Should you decide to uninstall cblaster, this can also be done using pip:

pip uninstall cblaster

Note: If a new version of cblaster is available, you can simply uninstall and reinstall the module as above to access the newer version.