Restructured instructions for clairty.

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nleo575 2020-03-06 16:46:25 -05:00
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Installation Installation
=============== ===============
This instructions have been tested on MacOS Catalina and Mojave and Ubuntu 16.04. If you find a problem, please report it. 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.
Mac OS (tested on Catalina) macOS (tested on Catalina 10.15)
---------------------------- --------------------------------
#. Install dependenies (Homebrew if not installed): #. Install dependenies (Homebrew if not installed):
@ -36,47 +36,17 @@ Mac OS (tested on Catalina)
#. Create a python virtual environment: #. Create a python virtual environment:
- ``cd rapids`` - ``cd rapids``
- ``conda env create -f environment.yml -n MY_ENV_NAME`` - ``conda env create -f environment.yml -n rapids``
- ``conda activate MY_ENV_NAME`` - ``conda activate rapids``
#. Install r packages and virtual environment: #. Install r packages and virtual environment:
- ``snakemake packrat_install`` - ``snakemake packrat_install``
- ``snakemake packrat_init`` - ``snakemake packrat_init``
- ``snakemake packrat_restore`` - ``snakemake packrat_restore``
- This step will take several minutes to complete. Please be patient and let it run until completion.
#. See Usage section below.
#. Configure the participants to analyze:
- Create a file per participant in the ``/data/external`` folder, no extension is necessary, its name will be the label for that participant in the pipeline: ``/data/external/pxx``
- Add a line with the device_id(s) of that participant as it appears on the database. If multiple device ids, all data for this participant will be relabeled with the last one
- Add a line with the mobile platform (android, or ios)
- For example:
.. code-block:: bash
3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9
android
#. Configure the db connection:
- Create an empty .env file in the root folder
- Add and complete the following lines:
| ``[MY_GROUP_NAME]``
| ``user=MyUSER``
| ``password=MyPassword``
| ``host=MyIP``
| ``port=3306``
#. 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.::
$ snakemake
This pulls sample data from AWARE_ and processes it with the default rules that come with RAPIDS.
Linux (tested on Ubuntu 16.04) Linux (tested on Ubuntu 16.04)
@ -117,22 +87,32 @@ Linux (tested on Ubuntu 16.04)
- ``snakemake packrat_install`` - ``snakemake packrat_install``
- ``snakemake packrat_init`` - ``snakemake packrat_init``
- ``snakemake packrat_restore`` - ``snakemake packrat_restore``
- This step will take several minutes to complete. Please be patient and let it run until completion.
#. Configure the participants to analyze: #. See Usage section below.
- Create a file per participant in the ``/data/external`` folder, no extension is necessary, its name will be the label for that participant in the pipeline: ``/data/external/pxx``
- Add a line with the device_id(s) of that participant as it appears on the database. If multiple device ids, all data for this participant will be relabeled with the last one Usage
- Add a line with the mobile platform (android, or ios) ======
- For example: Once you have the installation for your specific operating system complete, you can follow these steps to get starting using the pipeline.
#. Configure the participants you want to analyze:
- 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 a comma separated list with each of the device ID numbers for that participant as it appears in AWARE.
- If AWARE is removed and reinstalled on the device, a new device ID is generated.
- The second line should list the device's operating system (Android or iOS)
- 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:
.. code-block:: bash .. code-block:: bash
3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9 3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9
android android
#. Configure the db connection:
- Create an empty .env file in the root folder #. Configure the database connection:
- Create an empty file called `.env` in the root directory (rapids/)
- Add and complete the following lines: - Add and complete the following lines:
| ``[MY_GROUP_NAME]`` | ``[MY_GROUP_NAME]``
@ -140,18 +120,20 @@ Linux (tested on Ubuntu 16.04)
| ``password=MyPassword`` | ``password=MyPassword``
| ``host=MyIP`` | ``host=MyIP``
| ``port=3306`` | ``port=3306``
- Replace your database specific credentials with those listed above.
#. 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.:: #. 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.::
$ snakemake $ snakemake
This pulls sample data from AWARE_ and processes it with the default rules that come with RAPIDS. This pulls sample data from AWARE_ and processes it with the default rules that come with RAPIDS.
.. _the-install-note: .. _the-install-note:
.. note:: .. note::
- Ensure that ``MY_GROUP_NAME`` is the same value for GROUP in the ``DATABASE_GROUP`` variable in the ``config.yaml`` file. - Ensure that ``MY_GROUP_NAME`` is the same value for GROUP in the ``DATABASE_GROUP`` variable in the ``config.yaml`` file located in the root directory (rapids/config.yaml).
- 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) - 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)