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Installation
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We recommend running bulkvis from within a python virtual environment so that there are no conflicts in dependencies.

Installing pip
==============

pip is most likely already installed, to find out run::

    pip --version

If pip is not installed, use the official
`get-pip.py <https://pip.pypa.io/en/stable/installing/#installing-with-get-pip-py>`_ script.

Create and activate a virtual environment
=========================================

For linux and MacOS::

    python3 -m venv bulkvis-env
    source bulkvis-env/bin/activate

For Windows::

    python3 -m venv bulkvis
    bulkvis\Scripts\activate

If the virtual environment is successfully activated the prefix ``(bulkvis)`` will be present.

Running ``deactivate`` will deactivate and exit the virtual environment

Clone bulkvis
=============

bulkvis can be retrieved by cloning the git repository::

    git clone https://github.com/LooseLab/bulkvis.git

or by navigating to `bulkvis <https://github.com/LooseLab/bulkvis.git>`_ and downloading an zip of the repository,
this will then need to be unzipped.

Installing dependencies
=======================

Once the repository is cloned or downloaded bulkvis' dependencies will need to be installed. This **must** be run from
within the virtual environment to prevent conflicts. Run::

    pip install -r bulkvis/requirements.txt

This will fetch and install all the required packages.

Creating config.ini
===================

bulkvis uses a configuration file, config.ini, to provide global variables that are required for operation. A config
file can either be generated by running ``utils/set_config.py`` (requires a bulkfile) or by copying and editing an
example bulkfile from ``config.md``.

Using ``set_config.py``::

    cd bulkvis
    python utils/set_confi.py -b <<bulkfile>> -i /path/to/bulkfile/directory -e /path/to/readfile/directory -m /path/to/mapfile/directory -c config.ini

Using ``config.md``::

    cd bulkvis
    touch config.ini
    nano config.ini

Then navigate to `config.md <https://github.com/LooseLab/bulkvis/blob/master/config.md>`_, copy and paste the example
configuration settings into nano in the terminal and finally change the directories (``dir``, ``out`` and ``map``) to point
towards your bulk-fast5-files and a read directory.

Starting bulkvis
================

To start bulkvis::

    bokeh serve --show bulkvis