Restructured instructions for clairty.
nleo575
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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.
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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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Mac OS (tested on Catalina)
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----------------------------
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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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@ -36,47 +36,17 @@ Mac OS (tested on Catalina)
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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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- ``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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#. Configure the participants to analyze:
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- 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``
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- 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
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- Add a line with the mobile platform (android, or ios)
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- For example:
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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 db connection:
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- Create an empty .env file in the root folder
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- Add and complete the following lines:
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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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#. 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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#. See Usage section below.
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Linux (tested on Ubuntu 16.04)
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@ -117,22 +87,32 @@ Linux (tested on Ubuntu 16.04)
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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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#. Configure the participants to analyze:
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#. See Usage section below.
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- 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``
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- 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
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- Add a line with the mobile platform (android, or ios)
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- For example:
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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 db connection:
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- Create an empty .env file in the root folder
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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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| ``[MY_GROUP_NAME]``
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@ -140,18 +120,20 @@ Linux (tested on Ubuntu 16.04)
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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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#. 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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.. _the-install-note:
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.. note::
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- Ensure that ``MY_GROUP_NAME`` is the same value for GROUP in the ``DATABASE_GROUP`` variable in the ``config.yaml`` file.
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- 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).
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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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