145 lines
4.9 KiB
ReStructuredText
145 lines
4.9 KiB
ReStructuredText
.. _install-page:
|
|
|
|
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.
|
|
|
|
macOS (tested on Catalina 10.15)
|
|
--------------------------------
|
|
|
|
#. Install dependenies (Homebrew if not installed):
|
|
|
|
- Install brew_ for Mac: ``/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"``
|
|
|
|
#. Install MySQL
|
|
|
|
- ``brew install mysql``
|
|
- ``brew services start mysql``
|
|
|
|
#. Install R, pandoc and rmarkdown:
|
|
|
|
- ``brew install r``
|
|
- ``brew install pandoc``
|
|
- ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
|
|
|
|
#. Install miniconda:
|
|
|
|
- ``brew cask install miniconda``
|
|
- ``conda init zsh`` or ``conda init bash``
|
|
- Restart terminal if necessary
|
|
|
|
#. Clone our repo:
|
|
|
|
- ``git clone https://github.com/carissalow/rapids``
|
|
|
|
#. Create a python virtual environment:
|
|
|
|
- ``cd rapids``
|
|
- ``conda env create -f environment.yml -n rapids``
|
|
- ``conda activate rapids``
|
|
|
|
#. Install r packages and virtual environment:
|
|
|
|
- ``snakemake packrat_install``
|
|
- ``snakemake packrat_init``
|
|
- ``snakemake packrat_restore``
|
|
- This step will take several minutes to complete. Please be patient and let it run until completion.
|
|
|
|
#. See Usage section below.
|
|
|
|
|
|
Linux (tested on Ubuntu 16.04)
|
|
------------------------------
|
|
|
|
#. Install dependenies (Homebrew - if not installed):
|
|
|
|
- ``sudo apt-get install libmariadb-client-lgpl-dev libxml2-dev libssl-dev``
|
|
- Install brew_ for linux and add the following line to ~/.bashrc: ``export PATH=$HOME/.linuxbrew/bin:$PATH``
|
|
- ``source ~/.bashrc``
|
|
|
|
#. Install MySQL
|
|
|
|
- ``brew install mysql``
|
|
- ``brew services start mysql``
|
|
|
|
#. Install R, pandoc and rmarkdown:
|
|
|
|
- ``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_
|
|
|
|
#. Clone our repo:
|
|
|
|
- ``git clone https://github.com/carissalow/rapids``
|
|
|
|
#. Create a python virtual environment:
|
|
|
|
- ``cd rapids``
|
|
- ``conda env create -f environment.yml -n MY_ENV_NAME``
|
|
- ``conda activate MY_ENV_NAME``
|
|
|
|
#. 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.
|
|
|
|
|
|
Usage
|
|
======
|
|
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 database connection:
|
|
|
|
- Create an empty file called `.env` in the root directory (rapids/)
|
|
- Add and complete the following lines:
|
|
|
|
| ``[MY_GROUP_NAME]``
|
|
| ``user=MyUSER``
|
|
| ``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 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)
|
|
|
|
|
|
|
|
|
|
.. _bug: https://github.com/Homebrew/linuxbrew-core/issues/17812
|
|
.. _instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
|
|
.. _brew: https://docs.brew.sh/Homebrew-on-Linux
|
|
.. _AWARE: https://awareframework.com/what-is-aware/ |