diff --git a/nesoni.rb b/nesoni.rb new file mode 100644 index 0000000..6135acc --- /dev/null +++ b/nesoni.rb @@ -0,0 +1,59 @@ +class Nesoni < Formula + homepage "http://www.bioinformatics.net.au/software.nesoni.shtml" + url "https://github.com/Victorian-Bioinformatics-Consortium/nesoni/archive/v0.130.tar.gz" + version "0.130" + sha1 "4077a992dfc519f3bd6a73fe76e4b90eb5ccc705" + + # For matplotlib + depends_on "freetype" + depends_on "samtools" + depends_on "shrimp" + + resource "numpy" do + url "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.2.tar.gz" + sha1 "86b4414cd01c4244141c59ea476ca8fdad8e9be2" + end + + resource "matplotlib" do + url "https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.4.3.tar.gz" + sha1 "8b24472780a23e686135dd08ec1bc5ef88db1979" + end + + resource "biopython" do + url "https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz" + sha1 "16dc84622a707118b3cd48c09807810de61d2321" + end + + + def install + ENV.prepend_create_path "PYTHONPATH", libexec/"vendor/lib/python2.7/site-packages" + %w[numpy matplotlib biopython].each do |r| + resource(r).stage do + system "python", *Language::Python.setup_install_args(libexec/"vendor") + end + end + + ENV.prepend_create_path "PYTHONPATH", libexec/"lib/python2.7/site-packages" + system "python", *Language::Python.setup_install_args(libexec) + + bin.install Dir["#{libexec}/bin/*"] + bin.env_script_all_files(libexec/"bin", :PYTHONPATH => ENV["PYTHONPATH"]) + end + + + def caveats + <<-EOS.undent + + 1) Nesoni has been installed without the dependencies required for VCF calling: + * Picard + * Freebayes + * SplitsTree4 + 2) We also ignore R libraries (we don't do RNA-Seq) + EOS + end + + + test do + system "#{bin}/nesoni", "clip" + end +end