Quick Start =========== This page covers installing RAFT (the workflow manager that runs LENS) and running a built-in demonstration. By the end of this page you will have LENS running on real patient data. Installing RAFT _______________ RAFT is the Nextflow-based workflow manager that runs LENS. More information about RAFT is available at `useraft.io `_. Installing through Conda ~~~~~~~~~~~~~~~~~~~~~~~~ Ensure Conda is installed prior to installing RAFT. Installation instructions are available on the `Conda documentation page `_. .. code-block:: console $ conda install -c bioconda -c conda-forge -c raft reproducible-analyses-framework-and-tools Installing through pip ~~~~~~~~~~~~~~~~~~~~~~ Installing RAFT through ``pip`` requires separately installing `Apptainer `_ and `Git `_. .. code-block:: console $ pip install --user reproducible-analyses-framework-and-tools .. note:: ``pip`` will install ``raft`` to ``~/.local/bin``. Please ensure this directory is in your ``$PATH`` (``export PATH=$PATH:~/.local/bin``). Setting up RAFT _______________ RAFT requires a directory consisting of various folders including: ``/Projects``, ``/References``, and ``/Metadata``. This directory will also contain the RAFT configuration file. To set up RAFT, run: .. code-block:: console $ raft.py setup You will be prompted to provide paths for each required subdirectory (with sensible defaults). A default installation (in which all subdirectories are created in the user's current working directory) can be created by running: .. code-block:: console $ raft.py setup --default .. note:: Users installing with the ``--default`` option should ensure their working directory does not have unreasonable (e.g. < 1 TB) storage limitations. Running the demonstration _________________________ The LENS demonstration provides an end-to-end example using a melanoma patient (``Pt01``) from the dataset associated with `Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma `_ (Hugo et al., 2016). To run the demonstration, ``cd`` to your ``raft/`` directory and run: .. code-block:: console $ raft.py run-demo --workflow lens --version 1.9-dev This will: - Create a project named ``demo-lens-v1.9-dev`` in ``./raft/projects`` - Download the required RAFT modules - Download the demo references, sample-level FASTQs, and sample manifest - Run the project's workflow During execution, you will see progress messages such as: .. code-block:: console Initializing project demo-lens... Pulling off-the-shelf workflow... This may take some time due to module fetching. Loading manifest... Loading references... ... All human references downloaded successfully! Loading fastqs... Building workflow... Connecting subworkflows... Populating default parameters... Running workflow... The resulting project will be stored in ``/path/to/raft/projects/demo-lens-v1.9-dev/``. What's next? ____________ After the demonstration completes: - See :doc:`accessing_and_reviewing_outputs` for an overview of what LENS produces - See :doc:`interpreting_report` for guidance on reading the LENS report - See :doc:`preparing_your_samples` to prepare your own sample manifest - See :doc:`running_lens` to run LENS on your own data