Added the Quick Rule Page

pull/95/head
kaguillera 2020-03-09 17:07:51 -04:00
parent 83d241e6ff
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usage/introduction usage/introduction
usage/installation usage/installation
usage/quick_rule
usage/snakemake_docs usage/snakemake_docs
.. toctree:: .. toctree::

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Quick Rule
=============
The following is a quick guide for creating and running a simple rule.
#. Setup database connection credential the ``.env``. See step 1 under the :ref:`Usage Section of Install <db-configuration>` page.
#. Create at least one participant file ``p01`` in the ``data/external``. See step 2 under the :ref:`Usage Section of Install <db-configuration>` page.
#. Activate the Conda (python) environment. See install step 2 on :ref:`install-page` page.
#. Prepare the ``Snakefile`` by replacing the code in the ``Snakefile`` with the following
::
configfile: "config.yaml"
include: "rules/packrat.snakefile"
include: "rules/preprocessing.snakefile"
include: "rules/features.snakefile"
include: "rules/reports.snakefile"
rule all:
input:
expand("data/processed/{pid}/call_{call_type}_{day_segment}.csv",
pid=config["PIDS"],
call_type=config["CALLS"]["TYPES"],
day_segment = config["CALLS"]["DAY_SEGMENTS"]),
#. Prepare the ``config.yaml`` changing the following settings only to values shown below (leave all other settings as they are)
::
SENSORS: [calls]
FITBIT_TABLE: []
FITBIT_SENSORS: []
PIDS: [p01]
DAY_SEGMENTS: &day_segments
[daily, night]
TIMEZONE: &timezone
America/New_York
DATABASE_GROUP: &database_group
MY_GROUP
For more information on the ``calls`` sensor see :ref:`call-sensor-doc`
#. Run the following command to execute the rule
::
snakemake
#. The results of the execution of the rule will be found in the ``data/processed/p01`` directory.