146 lines
5.1 KiB
ReStructuredText
146 lines
5.1 KiB
ReStructuredText
.. _install-page:
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Installation
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===============
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This instructions have been tested on macOS (Catalina and Mojave) and Ubuntu 16.04. If you find a problem, please report it on our GitHub page.
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macOS (tested on Catalina 10.15)
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--------------------------------
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#. Install dependenies (Homebrew if not installed):
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- Install brew_ for Mac: ``/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"``
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#. Install MySQL
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- ``brew install mysql``
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- ``brew services start mysql``
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#. Install R, pandoc and rmarkdown:
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- ``brew install r``
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- ``brew install pandoc``
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- ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
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#. Install miniconda:
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- ``brew cask install miniconda``
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- ``conda init zsh`` or ``conda init bash``
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- Restart terminal if necessary
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#. Clone our repo:
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- ``git clone https://github.com/carissalow/rapids``
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#. Create a python virtual environment:
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- ``cd rapids``
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- ``conda env create -f environment.yml -n rapids``
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- ``conda activate rapids``
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#. Install r packages and virtual environment:
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- ``snakemake packrat_install``
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- ``snakemake packrat_init``
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- ``snakemake packrat_restore``
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- This step will take several minutes to complete. Please be patient and let it run until completion.
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#. See Usage section below.
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Linux (tested on Ubuntu 16.04)
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------------------------------
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#. Install dependenies (Homebrew - if not installed):
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- ``sudo apt-get install libmariadb-client-lgpl-dev libxml2-dev libssl-dev``
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- Install brew_ for linux and add the following line to ~/.bashrc: ``export PATH=$HOME/.linuxbrew/bin:$PATH``
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- ``source ~/.bashrc``
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#. Install MySQL
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- ``brew install mysql``
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- ``brew services start mysql``
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#. Install R, pandoc and rmarkdown:
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- ``brew install r``
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- ``brew install gcc@6`` (needed due to this bug_)
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- ``HOMEBREW_CC=gcc-6 brew install pandoc``
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- ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
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#. Install miniconda using these instructions_
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#. Clone our repo:
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- ``git clone https://github.com/carissalow/rapids``
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#. Create a python virtual environment:
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- ``cd rapids``
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- ``conda env create -f environment.yml -n MY_ENV_NAME``
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- ``conda activate MY_ENV_NAME``
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#. Install r packages and virtual environment:
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- ``snakemake packrat_install``
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- ``snakemake packrat_init``
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- ``snakemake packrat_restore``
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- This step will take several minutes to complete. Please be patient and let it run until completion.
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#. See Usage section below.
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Usage
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======
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Once you have the installation for your specific operating system complete, you can follow these steps to get starting using the pipeline.
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#. Configure the participants you want to analyze:
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- Create one file per participant in the ``rapids/data/external/`` directory. The file should NOT have an extension (i.e. no .txt). The name of the file will become the label for that participant in the pipeline.
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- The first line of the file should be a comma separated list with each of the device ID numbers for that participant as it appears in AWARE.
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- If AWARE is removed and reinstalled on the device, a new device ID is generated.
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- The second line should list the device's operating system (Android or iOS)
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- As an example. Let's say participant `p00` had 2 AWARE device_id numbers and was running Android OS. Their file would be named `p00` and contain:
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.. code-block:: bash
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3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9
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android
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#. Configure the database connection:
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- Create an empty file called `.env` in the root directory (``rapids/``)
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- Add and complete the following lines:
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.. code-block:: bash
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[MY_GROUP_NAME]
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user=MyUSER
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password=MyPassword
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host=MyIP
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port=3306
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- Replace your database specific credentials with those listed above.
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- ``MY_GROUP_NAME`` is a custom label you assign when setting up the database configuration. It does not have to relate to your
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.. _the-install-note:
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.. note::
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- ``MY_GROUP_NAME`` must also be assigned to the ``DATABASE_GROUP`` variable in the ``config.yaml`` file, which is located in the root directory (``rapids/config.yaml``).
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- Ensure that your list of ``SENSORS`` in the ``config.yaml`` file correspond to the sensors used in the ``all`` rule in the ``Snakefile`` file (See :ref:`rapids-structure` for more information)
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#. Once the all of the installation and configurations has been completed the following command can be run to pull the default sample dataset that comes with this project.::
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$ snakemake
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This pulls sample data from AWARE_ and processes it with the default rules that come with RAPIDS.
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.. _bug: https://github.com/Homebrew/linuxbrew-core/issues/17812
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.. _instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
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.. _brew: https://docs.brew.sh/Homebrew-on-Linux
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.. _AWARE: https://awareframework.com/what-is-aware/ |