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salmon.rb
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salmon.rb
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class Salmon < Formula
desc "Transcript-level quantification from RNA-seq reads"
homepage "https://github.com/COMBINE-lab/salmon"
# tag "bioinformatics"
url "https://github.com/COMBINE-lab/salmon/archive/v0.8.2.tar.gz"
sha256 "299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91"
head "https://github.com/COMBINE-lab/salmon.git"
bottle do
cellar :any
sha256 "c8acb85e67e81d6bd2bedcd408937cc92e09d7a2a4d0ff56fbf4448736d9b052" => :el_capitan
sha256 "1ba278c961a7f5bd0d22128c28c8fc8ab6bbdebce30b5f636d10a1c180b493aa" => :yosemite
sha256 "4341b6d73b4c99ca6dbabd4a2f708cf7d7ef1fa5af1df4b6cb1ce7a26327cd39" => :mavericks
sha256 "8872fe59fa76b0c76db2fa31599ac25830d67136afc84235b704a696f40d360e" => :x86_64_linux
end
# See https://github.com/kingsfordgroup/sailfish/issues/74
needs :cxx11
depends_on "autoconf" => :build
depends_on "automake" => :build
depends_on "cmake" => :build
depends_on "boost"
depends_on "tbb"
depends_on "xz"
depends_on "zlib" unless OS.mac?
def install
# Fix error: Unable to find the requested Boost libraries.
ENV.deparallelize
# Fix wonky clang reporting itself as GCC
if ENV.compiler == :clang && MacOS.version <= :mavericks
inreplace "include/concurrentqueue.h",
"typedef ::max_align_t max_align_t",
"typedef std::max_align_t max_align_t"
end
system "cmake", ".", *std_cmake_args
system "make", "install"
end
test do
system "#{bin}/salmon", "--version"
end
end