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imac_setup.md

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Instructions for setting up iMacs at CSHL

Author: Olga Botvinnik
Email: [email protected]
Date: 2016-06-06

This document sets up fresh iMacs with no bioinformatics tools to be ready for running alignments and counting reads.

    1. Start downloading a gzip of all the data
curl https://s3-us-west-2.amazonaws.com/single-cell-bioinformatics/data.tar.gz > single-cell-bioinformatics-data.tar.gz
    1. Open a new tab and download latest Miniconda for Python3 and save as miniconda.sh
curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh
    1. Install Miniconda with defaults (-b flag) into specific folder
bash miniconda.sh -b -p $HOME/miniconda
    1. Add ~/miniconda/bin to $PATH
export PATH="$HOME/miniconda/bin:$PATH"
conda config --add channels r
conda config --add channels bioconda
    1. Install Bioinformatics packages
conda install --yes STAR samtools subread bedtools cutadapt fastqc
    1. Unzip the data. This creates a folder called single-cell-bioinformatics
tar xzvf single-cell-bioinformatics-data.tar.gz
    1. Move everything in the single-cell-bioinformatics folder down to the home folder
mv single-cell-bioinformatics-data/* ~/
    1. Remove the empty single-cell-bioinformatics-data folder
rm -rf single-cell-bioinformatics-data