diff --git a/docs/usage/installation.rst b/docs/usage/installation.rst index 5d22c63d..e5422c74 100644 --- a/docs/usage/installation.rst +++ b/docs/usage/installation.rst @@ -3,7 +3,7 @@ Installation =============== -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. +These instructions have been tested on macOS (Catalina and Mojave) and Ubuntu 16.04. If you find a problem, please create a GitHub issue or contact us. macOS (tested on Catalina 10.15) -------------------------------- @@ -17,11 +17,10 @@ macOS (tested on Catalina 10.15) - ``brew install mysql`` - ``brew services start mysql`` -#. Install R, pandoc and rmarkdown: +#. Install R and pandoc: - ``brew install r`` - ``brew install pandoc`` - - ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'`` #. Install miniconda: @@ -44,7 +43,7 @@ macOS (tested on Catalina 10.15) - ``snakemake renv_install`` - ``snakemake renv_init`` - ``snakemake renv_restore`` - - This step will take several minutes to complete. Please be patient and let it run until completion. + - This step could take several minutes to complete. Please be patient and let it run until completion. #. See Usage section below. @@ -68,7 +67,6 @@ Linux (tested on Ubuntu 16.04) - ``brew install r`` - ``brew install gcc@6`` (needed due to this bug_) - ``HOMEBREW_CC=gcc-6 brew install pandoc`` - - ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'`` #. Install miniconda using these instructions_ @@ -87,47 +85,47 @@ Linux (tested on Ubuntu 16.04) - ``snakemake renv_install`` - ``snakemake renv_init`` - ``snakemake renv_restore`` - - This step will take several minutes to complete. Please be patient and let it run until completion. + - This step could take several minutes to complete. Please be patient and let it run until completion. #. See Usage section below. Usage ====== -Once you have the installation for your specific operating system complete, you can follow these steps to start using RAPIDS. +Once RAPIDS is installed, follow these steps to start processing mobile data. .. _db-configuration: #. Configure the database connection: - Create an empty file called `.env` in the root directory (``rapids/``) - - Add the following lines and replace your database specific credentials (user, password, and host): + - Add the following lines and replace your database specific credentials (user, password, host, and database): .. code-block:: bash [MY_GROUP] - user=MyUSER - password=MyPassword - host=MyIP + user=MY_USER + password=MY_PASSWORD + host=MY_HOST port=3306 - database=MyDB + database=MY_DATABASE .. note:: - ``MY_GROUP`` is a custom label you assign when setting up the database configuration. It has to match ``DATABASE_GROUP`` in the ``config.yaml`` file_. It does not have to relate to your database credentials. + ``MY_GROUP`` is a custom label for your credentials. It has to match ``DATABASE_GROUP`` in the ``config.yaml`` file_. It is not related to your database configuration. -#. Configure the participants you want to analyze: +#. Setup the participants' devices whose data you want to analyze: - - **Automatically**. You can automatically include all devices that are stored in the ``aware_device`` table, if you have especial requirements see the Manual configuration:: + - **Automatically**. You can automatically include all devices that are stored in the ``aware_device`` table. If you have especial requirements see the Manual configuration:: - snakemake download_participants + snakemake -j1 download_participants - **Manually**. 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. - The first line of the file should be the Aware ``device_id`` for that participant. If one participant has multiple device_ids (i.e. Aware had to be re-installed), add all device_ids separated by commas. - The second line should list the device's operating system (``android`` or ``ios``) - - The third line is a human friendly label that will appear in any plots for that participant. - - The forth line contains a start and end date separated by a comma (e.g. ``20201301,20202505``). Only data wihtin these dates will be included in the pipeline. + - The third line is an optional human friendly label that will appear in any plots for that participant. + - The forth line is optional and contains a start and end date separated by a comma ``YYYYMMDD,YYYYMMDD`` (e.g. ``20201301,20202505``). Only data wihtin these dates will be included in the pipeline, if no dates are specified all data from that device will be included. For example, let's say participant `p01` had two AWARE device_ids and they were running Android between Feb 1st 2020 and March 3rd 2020. Their participant file would be named ``p01`` and contain: @@ -140,7 +138,7 @@ Once you have the installation for your specific operating system complete, you #. Configure the sensors to process: - - The variable ``SENSORS`` in the ``config.yaml`` file_ should match existent sensor tables in your Aware database (See :ref:`rapids-structure` for more information). Each item in this list will be processed in RAPIDS. + - The variable ``SENSORS`` in the ``config.yaml`` file_ should match existent sensor tables in your Aware database (See :ref:`rapids-structure` for more information). Each sensor in this list will be processed in RAPIDS. .. note::