PyInKnife2 is a Python package.
In order to install PyInKnife2 you will need Python 3.7 or higher, several open-source Python packages and PyInteraph2.
Python is usually available by default in any Linux installation, while the Python packages will be installed automatically during the installation process. Please see the requirements.txt file or the environment.yaml file for the complete list of Python packages required.
PyInteraph2 can be found here. PyInteraph2 needs to be installed before proceeding with the installation of PyInKnife2. Detailed installation instructions regarding how to install both PyInteraph2 and PyInKnife2 are provided below.
Here, we provide instructions for installing PyInteraph2 and PyInKnife2 in a simple Python environment or in a conda environment.
This is a simple installation procedure that requires a Python >= 3.7 distribution to be available. It guides you in the installation of the PyInKnife2 package in a virtual environment, meaning an instance of Python isolated from the rest of your system.
This is not strictly necessary and PyInKnife2 may be installed system-wide in a similar fashion, following steps 4 to 9.
As you will see from the instructions, PyInteraph2 is installed before PyInKnife2.
Check if the virtualenv Python package is installed in your system.
If the virtualenv command is available to you, it is installed and you can skip this step.
If it is not available and you need to install it, it is usually available as a package in your distribution. For instance, on Debian-based systems (such as Debian or Ubuntu) this boils down to installing the python-virtualenv package:
sudo apt install python-virtualenvIf this is not possible for you, you may still install the virtualenv package for just your local user, using pip:
pip install --user virtualenvIf the installation is successful, the virtualenv command will be available.
Create your Python 3.7 virtual environment, in a directory of your choice (in this case, it will be ./pyinknife2-env):
virtualenv -p /usr/bin/python3.7 pyinknife2-envYou might need to replace the argument of option -p according to the location of your Python installation in the system.
Activate the environment:
source pyinknife2-env/bin/activateClone the PyInteraph2 source code from its GitHub repository and enter the local copy of the repository.
git clone https://github.com/ELELAB/pyinteraph2.git
cd pyinteraph2If git is not available to you, you can download the repository content as a ZIP file from the PyInteraph2 GitHub repository web page.
Install all the required Python packages as specified in the requirements.txt file in the pyinteraph2 directory via pip:
pip install -r requirements.txtYou can now install PyInteraph2:
python setup.py install
cd ..PyInteraph2 is now installed and you can proceed to the installation of PyInKnife2.
Clone the PyInKnife2 source code from its GitHub repository and enter the local copy of the repository.
git clone https://github.com/ELELAB/PyInKnife2.git
cd PyInKnife2If git is not available to you, you can download the repository content as a ZIP file from the PyInKnife2 GitHub repository web page.
Install all the required Python packages as specified in the requirements.txt file in the PyInKnife2 directory via pip:
pip install -r requirements.txtYou can now install PyInKnife2:
python setup.py installThat's it! The main PyInKnife2 executables (pyinknife_run, pyinknife_aggregate, pyinknife_plot) should now be available.
Every time you need to run PyInKnife2 after opening a new shell, just run step 3 beforehand.
Clone the PyInKnife2 source code from its GitHub repository and enter the local copy of the repository.
git clone https://github.com/ELELAB/PyInKnife2.gitIf git is not available to you, you can download the repository content as a ZIP file from the PyInKnife2 GitHub repository web page.
We have provided an environment.yaml file that can be used together with conda to automatically install an environment contaning all of PyInteraph2 and PyInKnife2's requirements.
In order to use it you need to have conda installed in your system. Go here for further instructions. Installing miniconda rather than full anaconda is advised.
Once conda is installed on your system, you can use it to create a virtual environment similarly to what you would do using the virtualenv package, as previously detailed.
Create your conda environment starting from the provided environment file:
conda env create --file PyInKnife2/environment.yaml --prefix ./pyinknife2-envIn this case we are asking conda to create the environment locally (--prefix). This is not strictly necessary.
Note that if your home directory is size-constrained the installation might fail for lack of space. In that case, you need to select another directory with more space available in which conda will download packages. This is done by running:
conda config --add pkgs_dirs /my/other/directory/conda/pkgsand changing /my/other/directory/conda/pkgs to a directory of your choice.
Activate the conda environment by running the command line that conda suggests for this purpose at the end of the previous step. It is usually something like:
conda activate ./pyinknife2-envClone the PyInteraph2 source code from its GitHub repository and enter the local copy of the repository.
git clone https://github.com/ELELAB/pyinteraph2.git
cd pyinteraph2If git is not available to you, you can download the repository content as a ZIP file from the PyInteraph2 GitHub repository web page.
You can now install PyInteraph2:
python setup.py installPyInteraph2 is now installed and you can proceed to the installation of PyInKnife2.
You can now install PyInKnife2:
cd ..
cd PyInKnife2
python setup.py installThat's it! The main PyInKnife2 executables (pyinknife_run, pyinknife_aggregate, pyinknife_plot) should now be available.
Every time you need to run PyInKnife2 after opening a new shell, just run step 4 beforehand.