If you want to try doing the labs directly on your Mac instead of in Virtual Box here is how you can.
Install the following packages by clicking on the link and following the instructions on the web page:
- Xcode, allowing compilation of source packages on your Mac.
- The atom editor
- The R statistical programming language
- The R IDE Rstudio
- The sequence alignment viewer jalview
- The network viewer cytoscape
Open up at 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
Install Homebrew, a package manager for OS X that it much easier to install Linux/Unix packages. There are some reports that homebrew has issues on El Capitan, but that may have been resolved. Let me know if you get data one way or the other.
From a terminal window:
brew update brew upgrade
install the following packages through homebrew
brew tap homebrew/science # additional packages brew install htop brew install git brew install igv brew install clustal-w brew install kalign brew install t-coffee brew install muscle brew install mafft brew install tophat brew install bwa brew install cufflinks brew install samtools brew install bedtools brew install blast brew install emboss
Open R and then
install.packages(c("swirl","ggplot2","genetics","LDheatmap","hwde","GenABEL","seqinr","qtl")) install.packages(c("evaluate","formatR","highr","markdown", "yaml","htmltools","caTools","bitops","knitr","rmarkdown")) install.packages("devtools") install.packages("shiny") install.packages("rsconnect") devtools::install_github(repo = "cran/PSMix") install.packages(c("pvclust","gplots","cluster","igraph","scatterplot3d","ape","SNPassoc"))
Still within R, install bioconductor
source("http://bioconductor.org/biocLite.R") biocLite() biocLite("edgeR") biocLite("VariantAnnotation")
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
Still need to deal with trimmomatic and auto_barcode, but the instructions in the labs should more or less work.