diff --git a/docs/usage/installation.rst b/docs/usage/installation.rst index a8d103cb..1d8b8141 100644 --- a/docs/usage/installation.rst +++ b/docs/usage/installation.rst @@ -1,54 +1,115 @@ Installation =============== -This instructions have been tested on MacOS Cataline and Ubuntu 16.04. If you find a problem, please report it. +This instructions have been tested on MacOS Catalina and Ubuntu 16.04. If you find a problem, please report it. -Install MySQL +Mac OS (tested on Catalina) +---------------------------- -- ``brew install mysql`` -- ``brew services start mysql`` +#. Install MySQL -Install R and rmarkdown: + - ``brew install mysql`` + - ``brew services start mysql`` -- ``brew install r`` -- ``brew install pandoc`` -- ``R -e 'install.packages(c( "rmarkdown"))'`` +#. Install R, pandoc and rmarkdown: -Install miniconda: + - ``brew install r`` + - ``brew install pandoc`` + - ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'`` -For Mac: +#. Install miniconda: + - ``brew cask install miniconda`` + - ``conda init zsh`` or ``conda init bash`` + - Restart terminal if necessary -- ``brew cask install miniconda`` -- ``conda init zsh`` or - ``conda init bash`` - -Clone our repo: +#. Clone our repo: -- ``git clone https://github.com/carissalow/moshi-aware-pipeline`` + - ``git clone https://github.com/carissalow/moshi-aware-pipeline`` -Create a python virtual environment: +#. Create a python virtual environment: -- ``conda env create -f environment.yml`` -- Restart terminal if necessary -- ``conda activate moshi-env`` + - ``conda env create -f environment.yml -n MY_ENV_NAME`` + - ``conda activate MY_ENV_NAME`` -Install r packages and virtual environment: +#. Install r packages and virtual environment: -- ``snakemake packrat_install`` -- ``snakemake packrat_init`` -- ``snakemake packrat_restore`` + - ``snakemake packrat_install`` + - ``snakemake packrat_init`` + - ``snakemake packrat_restore`` -Configure the participants to analyze: +#. Configure the participants to analyze: -- Add a file per participant and name it with the label for that participant, no extension is necessary: ``/data/external/pxx`` -- Add a line with the device_id for that participant as it appears on the db -- Add a line with the mobile platform (Android, or iOS) + - 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 -Configure the db connection: + 3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9 + android -- 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`` +#. 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`` + +Linux (tested on Ubuntu 16.04) +------------------------------ + +#. 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/moshi-aware-pipeline`` + +#. Create a python virtual environment: + + - ``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`` + +.. _bug: https://github.com/Homebrew/linuxbrew-core/issues/17812 +.. _instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html \ No newline at end of file