Update installation instructions
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Installation
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===============
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This instructions have been tested on MacOS Cataline and Ubuntu 16.04. If you find a problem, please report it.
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This instructions have been tested on MacOS Catalina and Ubuntu 16.04. If you find a problem, please report it.
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Install MySQL
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Mac OS (tested on Catalina)
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----------------------------
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- ``brew install mysql``
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- ``brew services start mysql``
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#. Install MySQL
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Install R and rmarkdown:
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- ``brew install mysql``
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- ``brew services start mysql``
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- ``brew install r``
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- ``brew install pandoc``
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- ``R -e 'install.packages(c( "rmarkdown"))'``
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#. Install R, pandoc and rmarkdown:
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Install miniconda:
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- ``brew install r``
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- ``brew install pandoc``
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- ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
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For Mac:
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#. Install miniconda:
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- ``brew cask install miniconda``
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- ``conda init zsh`` or ``conda init bash``
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- Restart terminal if necessary
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- ``brew cask install miniconda``
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- ``conda init zsh`` or - ``conda init bash``
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#. Clone our repo:
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Clone our repo:
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- ``git clone https://github.com/carissalow/moshi-aware-pipeline``
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- ``git clone https://github.com/carissalow/moshi-aware-pipeline``
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#. Create a python virtual environment:
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Create a python virtual environment:
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- ``conda env create -f environment.yml -n MY_ENV_NAME``
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- ``conda activate MY_ENV_NAME``
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- ``conda env create -f environment.yml``
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- Restart terminal if necessary
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- ``conda activate moshi-env``
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#. Install r packages and virtual environment:
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Install r packages and virtual environment:
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- ``snakemake packrat_install``
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- ``snakemake packrat_init``
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- ``snakemake packrat_restore``
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- ``snakemake packrat_install``
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- ``snakemake packrat_init``
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- ``snakemake packrat_restore``
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#. Configure the participants to analyze:
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Configure the participants to analyze:
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- 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``
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- 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
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- Add a line with the mobile platform (android, or ios)
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- For example:
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.. code-block:: bash
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- Add a file per participant and name it with the label for that participant, no extension is necessary: ``/data/external/pxx``
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- Add a line with the device_id for that participant as it appears on the db
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- Add a line with the mobile platform (Android, or iOS)
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3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9
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android
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Configure the db connection:
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#. Configure the db connection:
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- Create an empty .env file in the root folder
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- Add and complete the following lines
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- Create an empty .env file in the root folder
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- Add and complete the following lines
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| ``[MY_GROUP_NAME]``
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| ``user=MyUSER``
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| ``password=MyPassword``
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| ``host=MyIP``
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| ``port=3306``
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Linux (tested on Ubuntu 16.04)
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------------------------------
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#. Install MySQL
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- ``brew install mysql``
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- ``brew services start mysql``
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#. Install R, pandoc and rmarkdown:
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- ``brew install r``
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- ``brew install gcc@6`` (needed due to this bug_)
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- ``HOMEBREW_CC=gcc-6 brew install pandoc``
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- ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
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#. Install miniconda using these instructions_
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#. Clone our repo:
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- ``git clone https://github.com/carissalow/moshi-aware-pipeline``
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#. Create a python virtual environment:
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- ``conda env create -f environment.yml -n MY_ENV_NAME``
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- ``conda activate MY_ENV_NAME``
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#. Install r packages and virtual environment:
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- ``snakemake packrat_install``
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- ``snakemake packrat_init``
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- ``snakemake packrat_restore``
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#. Configure the participants to analyze:
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- 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``
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- 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
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- Add a line with the mobile platform (android, or ios)
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- For example:
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.. code-block:: bash
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3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9
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android
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#. Configure the db connection:
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- Create an empty .env file in the root folder
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- Add and complete the following lines
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| ``[MY_GROUP_NAME]``
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| ``user=MyUSER``
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| ``password=MyPassword``
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| ``host=MyIP``
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| ``port=3306``
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.. _bug: https://github.com/Homebrew/linuxbrew-core/issues/17812
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.. _instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
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