Installation ============ ``modality`` is currently supported on Linux and MacOS. Prerequisites ------------- The `Python programming language `_ is required to run ``modality``. Python version 3.11 is recommended, while version 3.10 is also supported. The ``modality.annotation`` submodule provides access to genomic data retrieved from GENCODE. To use it, the `HTSlib and Samtools `_ libraries need to be installed. .. _quickstart-label: Quickstart ---------- Below you can find a step-by-step guide to set up your environment and install ``modality``. We provide instructions for different levels of familiarity with Python and the command line. I have Python installed ^^^^^^^^^^^^^^^^^^^^^^^ If you already have Python installed, first create a Python virtual environment for your modality work, and then install ``modality`` using ``pip`` from the biomodal package repository: .. code-block:: bash # example for creating and activating a virtual environment # > python3 -m venv venv # > source venv/bin/activate # install modality pip install --extra-index-url https://europe-python.pkg.dev/prj-biomodal-modality/modality-pypi/simple modality HTSlib and Samtools can be installed with one of the following options: 1. From the `official source distribution `_. 2. Using `Conda `_ (packages `htslib `_ and `samtools `_ on the `bioconda` channel). 3. Using `Homebrew `_ (packages `htslib `_ and `samtools `_). I'm new to Python but familiar with the command line ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If you are comfortable working in the command line, the `pyenv `_ Python version manager would be a good choice to install Python. pyenv makes it easy to create and manage multiple Python environments for different projects from the command line. After installing pyenv, use it to install Python and create a virtual environment for your modality work: .. code-block:: bash # install Python 3.11 pyenv install 3.11 # create and activate a virtual environment pyenv virtualenv 3.11 modality # automatically activate the virtual environment in the modality project directory pyenv local modality # or manually activate the virtual environment # > pyenv activate modality # install modality pip install --extra-index-url https://europe-python.pkg.dev/prj-biomodal-modality/modality-pypi/simple modality Install HTSlib and Samtools from the `official source distribution `_. I'm new to Python and the command line ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If you are new to Python and are more comfortable with graphical programs than the command line, the `Anaconda distribution `_ is a good choice to install Python. Anaconda is free and open source, easy to use, includes many of the most popular Python packages for data exploration and analysis, and makes it easy to install popular bioinformatics and genomics tools. After installing Anaconda, create a virtual environment for your modality work using the commands below (in your terminal): .. code-block:: bash # create and activate virtual environment conda create --name modality python=3.11 conda activate modality # install modality pip install --extra-index-url https://europe-python.pkg.dev/prj-biomodal-modality/modality-pypi/simple modality Install HTSlib and Samtools with `conda` in the same virtual environment: .. code-block:: bash conda install -c bioconda htslib samtools .. raw:: html