Installing Requisite Software on your Mac

05 May 2020

If you want to try doing the labs directly on your Mac instead of on JetStream here is how you can. This document may have errors; please let me know and I can help (and update the document)

web downloads

Install the following packages by clicking on the link and following the instructions on the web page:

The atom editor
The R statistical programming language
The R IDE Rstudio
The sequence alignment viewer jalview # maybe not used
The network viewer cytoscape # maybe not used

Atom packages

Open up atom, click on File > Preferences, and then install the following atom packages. Not all of these are needed for the BIS180L but they are good to have

Sublime-Style_Column-Selection
language-markdown
git-plus
markdown-pdf
line-ending-converter

In Atom go to preferences and search for the ‘whitespace’ package. Disable it.

XCode command line tools

First you need to install Xcode, Apple’s development software that includes compilers necessary for installing packages from source.

We only need the Xcode command-line tools, you can install them by entering the command below in the Unix terminal:

xcode-select --install

(If you prefer, you can install the whole GUI instead but it takes up a lot of space and you will probably never use it.)

Homebrew

Homebrew is a package manager for OS X that it much easier to install Linux/Unix packages.

Go to the Homebrew webpage and follow the install instructions there.

After Homebrew is installed, then from a terminal window:

upgrade homebrew

brew update
brew upgrade

install the following packages through homebrew

brew tap brewsci/bio # additional packages
brew install htop
brew install wget
brew install git
brew cask install igv
brew install mafft
brew install bowtie2
brew install bwa
brew install bwa-mem2brew 
brew install samtools
brew install bedtools
brew install blast
brew install emboss
brew install gatk
brew install freebayes
brew install fasttree
brew install star
brew install fastqc
brew cask install dendroscope
brew cask install mega
brew cask install git-it

R packages

Open RStudio and then

install.packages(c('swirl','genetics','hwde','seqinr','qtl','evaluate','formatR','highr','markdown','yaml','htmltools','caTools','bitops','knitr','rmarkdown','devtools','shiny','pvclust','gplots','cluster','igraph','scatterplot3d','ape','SNPassoc','rsconnect','dplyr','tidyverse','learnr', 'LDheatmap'), dependencies=T)

Still within R, install Bioconductor

install.packages("BiocManager")
BiocManager::install(c("Rsubread","snpStats","rtracklayer","goseq","impute","multtest","VariantAnnotation","chopsticks","edgeR"))

perl modules

For auto_barcode to work, the following must be installed (From the Unix command line):

sudo cpan install Statistics::Descriptive
sudo cpan install Statistics::R
sudo cpan install Text::Levenshtein::XS
sudo cpan install Text::Table

tophat

cd /usr/local/bin
wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.OSX_x86_64.tar.gz
tar -xvzf tophat-2.1.1.OSX_x86_64.tar.gz
ln -s tophat-2.1.1.OSX_x86_64/tophat ./

add class data

IMPORTANT: I AM GIVING THIS A DIFFERENT PATH THAN USED IN THE LAB TO REDUCE THE CHANCE OF YOU OVERWRITING FILES ON YOUR COMPUTER. On the website it this is ~/data but here it is ~/bis180l/data. ``~/bis180l/data` will be overwritten so make sure that nothing critical is there.

cd
mkdir -p bis180l
cd bis180l
wget http://malooflab.phytonetworks.org/media/maloof-lab/filer_public/8f/d5/8fd59de6-e311-4d50-8320-acc58402982f/bis180l_class_data_2020tar.gz
tar xzvf bis180l_class_data_2020tar.gz
rm bis180l_class_data_2020tar.gz

Other

Still need to deal with trimmomatic and auto_barcode, but the instructions in the labs should more or less work.

fastStructure

I can’t get this to work, you will need to use your instance for this one.

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