ema 0.6.0 (new formula)

Fast and accurate alignment of linked reads

Formula/ema.rb

@@ -0,0 +1,40 @@
+class Ema < Formula
+  # cite Shajii_2017: "https://doi.org/10.1101/220236"
+  desc "Fast and accurate alignment of linked reads"
+  homepage "http://ema.csail.mit.edu"
+  url "https://github.com/arshajii/ema.git",
+    :tag => "0.6.0", :revision => "4e72fe2b1a207d9d5d75ecbf0a782987b3e9f250"
+  head "https://github.com/arshajii/ema"
+
+  fails_with :clang # needs openmp
+  needs :cxx14
+
+  if OS.mac?
+    depends_on "gcc" # needs openmp
+  else
+    depends_on "zlib"
+  end
+
+  resource "4M-with-alts" do
+    url "https://raw.githubusercontent.com/10XGenomics/supernova/master/tenkit/lib/python/tenkit/barcodes/4M-with-alts-february-2016.txt"
+    version "february-2016"
+    sha256 "47d7109416f06a7f4c78ed4b2dcb62682b5ca60edf421c687087d8084cf5f192"
+  end
+
+  def install
+    # Fix error: This file requires compiler and library support for the ISO C++ 2011 standard.
+    ENV.deparallelize
+
+    system "make"
+    bin.install "ema"
+    prefix.install resource("4M-with-alts")
+  end
+
+  def caveats
+    "The barcode whitelist is available at\n#{prefix/"4M-with-alts-february-2016.txt"}"
+  end
+
+  test do
+    assert_match "usage", shell_output("#{bin}/ema help")
+  end
+end