2019-12-12 00:29:57 +01:00
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Installation
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===============
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2019-12-12 00:44:37 +01:00
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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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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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Install MySQL
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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- ``brew install mysql``
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- ``brew services start mysql``
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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Install R:
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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- ``brew install r``
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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Install miniconda:
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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- ``brew cask install miniconda`` (for Mac)
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Clone our repo:
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:47:28 +01:00
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- ``git clone https://github.com/carissalow/moshi-aware-pipeline``
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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Create a python virtual environment:
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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- ``conda env create -f environment.yml``
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- ``conda init zsh/bash``
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- Restart terminal if necessary
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- ``conda activate moshi-env``
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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Install r packages and virtual environment:
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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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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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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Configure the participants to analyze:
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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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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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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Configure the db connection:
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2019-12-12 00:29:57 +01:00
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2019-12-12 00:44:37 +01:00
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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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