Homebrew repository for immune repertoire sequencing data analysis packages.
brew update
Make sure you have Java 1.8 installed. On MacOS you can use
brew cask install java
We'll also need some dependencies from Homebrew/Science:
brew tap homebrew/science
Installing RepSeq software bundle:
brew tap mikessh/repseq
brew install migec
brew install vdjtools
brew install vdjdb
# The following come separately for MacOS and Linux (linuxbrew)
brew install igblast-linux
brew install migmap-linux
brew install igblast-macos
brew install migmap-macos
This will install the software and make command line aliases: migec, vdjtools, etc.
To allocate more memory for Java (in case of Out Of Memory Errors), append -Xmx? option, e.g. migec -Xmx40G ....
N.B. If the script complains about BLAST already installed - use brew unlink blast