163 lines
5.2 KiB
ReStructuredText
163 lines
5.2 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.
|
|
|
|
Mac OS (tested on Catalina)
|
|
----------------------------
|
|
|
|
#. 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 MY_ENV_NAME``
|
|
- ``conda activate MY_ENV_NAME``
|
|
|
|
#. Install r packages and virtual environment:
|
|
|
|
- ``snakemake packrat_install``
|
|
- ``snakemake packrat_init``
|
|
- ``snakemake packrat_restore``
|
|
|
|
|
|
#. 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)
|
|
------------------------------
|
|
|
|
#. 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``
|
|
|
|
#. 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.
|
|
|
|
.. _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 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/ |