homebrew-core/Formula/kallisto.rb
2018-04-20 08:41:23 -07:00

44 lines
1.5 KiB
Ruby

class Kallisto < Formula
desc "Quantify abundances of transcripts from RNA-Seq data"
homepage "https://pachterlab.github.io/kallisto/"
url "https://github.com/pachterlab/kallisto/archive/v0.44.0.tar.gz"
sha256 "35a81201a56f4557697e6fe693dc6b701bbbd0a7b2b6e1c6c845ef816d67ca29"
revision 1
bottle do
cellar :any
sha256 "ab38b73fea94b87a8bb4a177a0c8d521bf91d5cd5476cd5b0237f2ea007ebefd" => :high_sierra
sha256 "aae08244ae475a38fe28b7d33b1ce48880f48e3905451e813ba88c9bf69eda77" => :sierra
sha256 "de0c2d1d3ec0b36aae9a536e890dab249bba372f26d6e72dc70d39e5ea3d29e9" => :el_capitan
end
depends_on "autoconf" => :build
depends_on "automake" => :build
depends_on "cmake" => :build
depends_on "hdf5"
def install
# Upstream issue 15 Feb 2018 "cmake does not run autoreconf for htslib"
# https://github.com/pachterlab/kallisto/issues/159
system "autoreconf", "-fiv", "ext/htslib"
system "cmake", ".", *std_cmake_args
# Upstream issue 15 Feb 2018 "parallelized build failure"
# https://github.com/pachterlab/kallisto/issues/160
# Upstream issue 15 Feb 2018 "cannot use system htslib"
# https://github.com/pachterlab/kallisto/issues/161
system "make", "htslib"
system "make", "install"
end
test do
(testpath/"test.fasta").write <<~EOS
>seq0
FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
EOS
output = shell_output("#{bin}/kallisto index -i test.index test.fasta 2>&1")
assert_match "has 1 contigs and contains 32 k-mers", output
end
end