homebrew_packages.yml

---
- hosts: all
  connection: local
  tasks:

    - name: Tap additional homebrew repositories we use
      homebrew_tap: name={{item}}
      with_items:
        - homebrew/science
        - homebrew/python
        - caskroom/cask
        - caskroom/fonts
      
    - name: Install cask dependencies (Java, Xquartz)
      homebrew_cask: name={{item}}
      with_items:
        - xquartz
        - java
     

    # Blast won't build with gcc-4.9 OR clang, lovely. I don't want to tap homebrew/versions
    ## - name: Install GCC 4.8 from homebrew/versions
    ##   shell: brew install homebrew/versions/gcc48 creates=/usr/local/bin/gcc-4.8

    - name: Install packages with homebrew
      homebrew: name={{item}} state=latest 
      with_items:
        - gcc 
        - git
        - wget
        - mosh
        - tmux
        - ack
        - mercurial
        - vim
        # From homebrew/science
        - blast
        - blat
        - samtools
        - bamtools
        - bedtools
        - bedops
        - bcftools
        - vcftools
        - htslib
        - bwa
        - bowtie
        - bowtie2
        - tophat
        - cufflinks
        - mummer
        - clustal-w
        - clustal-omega
        - fasta
        - fastqc
        - hmmer
        - igv
        - igvtools
        - meme
        - quast
        - lastz
        - abyss
        - igraph
        - picard-tools
        - trinity
        - velvet
        - ray
        - augustus
        - spades
        - soapdenovo
        - cegma
        # - glimmer3
        - glimmerhmm
        - gmap-gsnap
        - blasr
        - kraken
        - plink
        - quake
        - snpeff
        - hotspot
        - sratoolkit
        # From homebrew/python
        - numpy
        - scipy
        - matplotlib
        - pillow
        
    - name: Install packages with homebrew cask
      homebrew_cask: name={{item}} state=present 
      with_items:
        - font-dejavu-sans
        - dropbox
        - firefox
        - sublime-text
        - textmate
        - textwrangler
        - mactex
        - rstudio
        - atom
        - google-chrome