Home/Linuxbrew (tested on Ubuntu 14.04) formula for nesoni

nesoni.rb

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+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