title	author	numbersections	numbersubsections
GenomeCRISPR	Nourdine Bah	true	true

How to install and run the script

We assume that you are on bash, and that you have unzip and python3 already installed on your system. We also assume that black, pylint and pytest python packages are installed.

Extract the content of the zip archive

First, extract the content of the zip archive by running:

$ unzip genomecrispr.zip

This should create a folder called genomecrispr in your current directory.

Create package archive and generate documentation

Change directory to go to the genomecrispr folder and build the package by running:

$ cd genomecrispr
$ make build

The archive should be now visible in the dist directory:

$ ls dist
genomecrispr-0.0.0-py3-none-any.whl  genomecrispr-0.0.0.tar.gz

If you have sphinx and sphinx-rtd-theme installed, you can generated the documentation by running:

$ make doc

The generated documentation should be in genomecrispr/docs/build/html. You can now leave the genomecrispr directory and go back to where you were:

$ cd ../

Create a virtualenv environment

If you don't have virtualenv already on your system, please install it by running:

$ pip install virtualenv

Then, create a virtual environment called venv and source it by running:

$ virtualenv venv
$ . venv/bin/activate

You are now in the virtual environment.

Install the package

Now, install the package by running:

(venv) $ pip install genomecrispr/dist/genomecrispr-0.0.0.tar.gz

The package is now installed. You can display information about the script by running:

screen --help

Run the script

To run the script on a file you can run:

screen <PATH_OF_THE_FILE_CONTAINING_GENES> <BASE_PATH_OF_THE_RESULTS>

To run the solution on CDKs:

screen genomecrispr/cdks.txt results_cdks

Leave the virtual environment

When you are done, you can leave the virtual environment by running:

deactivate