(Optional) Additional Installations

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The installations below are only necessary for who looking to utilize the additional functionalities.

To solely utilize the main functionalities, skip this step.

Install the historef Package

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Only required if you want to align your histology images with the spatial digital gene expression (SGE) matrix.

Install the historef package in your Python environment. For the most recent version, please see its GitHub repository.

### activate your python environment
### Both the $pyenv_dir and $pyenv_name were defined in Configuring Python Virtual Environment.
source ${pyenv_dir}/$pyenv_name/bin/activate

### download the historef package
wget -P ${smk_dir}/installation https://github.com/seqscope/historef/releases/download/v0.1.3/historef-0.1.3-py3-none-any.whl

## install the historef package
pip install ${smk_dir}/installation/historef-0.1.3-py3-none-any.whl

Install the FICTURE Package

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Only required if you want to apply the SGE matrix filtering, reformatting or segmentation functionalities.

NovaScope has already included FICTURE as a submodule, but it is essential to install FICTURE and its dependencies into your Python virtual environment. For more details, please consult FICTURE's instructions.

## set the path to the python virtual environment directory
pyenv_dir=/path/to/python/virtual/environment/directory  ## provide the path of venv
pyenv_name=novascope_venv                                ## provide the name of the environment you created before

smk_dir=/path/to/the/novascope/directory

## activate the python environment (every time you want to use the environment)
source ${pyenv_dir}/${pyenv_name}/bin/activate

## install the required packages (need to be done only once)
pip install -r ${smk_dir}/submodules/ficture/requirements.txt

## install FICTURE
pip install ficture