Installation¶
Install¶
Note
NASP requires Python 3.
To install system-wide:
$ pip install nasp
One of the ways to install NASP as a user is in a python virtual environment. See the python documentation for alternative methods:
$ pyvenv my_env
$ source my_env/bin/activate
$ pip install nasp
If Python 2 is your default version, you should be able to run the Python 3 versions of pyvenv/pip explicitly:
$ pyvenv-3.4 my_env
$ source my_env/bin/activate
$ pip install nasp
The readline module is an optional dependency to enable tab-autocomplete when entering filepaths in NASP:
$ pip install readline
To learn more about installing python packages checkout the python documentation
Using the “module load” system: If you have configured a module system on your high-performance compute cluster, you can create a NASP module for your users to load. Refer to your operating system documentation for specifics. Do not forget to include the software dependencies, as described below.
Update¶
$ pip install --upgrade nasp
Uninstall¶
$ pip uninstall nasp
Dependencies¶
- Samtools < 1.3
- trimmomatic
- MUMmer >= 3.23