Restructured instructions for clairty.

docs/usage/installation.rst

@@ -3,10 +3,10 @@
 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):
 
@@ -36,47 +36,17 @@ Mac OS (tested on Catalina)
 #. Create a python virtual environment:
 
     - ``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:
 
     - ``snakemake packrat_install``
     - ``snakemake packrat_init``
     - ``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)
@@ -117,22 +87,32 @@ Linux (tested on Ubuntu 16.04)
     - ``snakemake packrat_install``
     - ``snakemake packrat_init``
     - ``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
 
             3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9
             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:
 
         | ``[MY_GROUP_NAME]``
@@ -140,18 +120,20 @@ Linux (tested on Ubuntu 16.04)
         | ``password=MyPassword``
         | ``host=MyIP``
         | ``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.::
 
     $ snakemake
 
+
 This pulls sample data from AWARE_ and processes it with the default rules that come with RAPIDS.
 
 .. _the-install-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)