imac_setup.md

Instructions for setting up iMacs at CSHL

Author: Olga Botvinnik
Email: olgabot@ucsd.edu
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

• 2. 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

• 2. Install Miniconda with defaults (-b flag) into specific folder

bash miniconda.sh -b -p $HOME/miniconda

• 3. Add ~/miniconda/bin to $PATH

export PATH="$HOME/miniconda/bin:$PATH"

• 4. Add R and Bioconda channels

conda config --add channels r
conda config --add channels bioconda

• 5. Install Bioinformatics packages

conda install --yes STAR samtools subread bedtools cutadapt fastqc

• 6. Unzip the data. This creates a folder called single-cell-bioinformatics

tar xzvf single-cell-bioinformatics-data.tar.gz

• 7. Move everything in the single-cell-bioinformatics folder down to the home folder

mv single-cell-bioinformatics-data/* ~/

• 8. Remove the empty single-cell-bioinformatics-data folder

rm -rf single-cell-bioinformatics-data