43 lines
1.5 KiB
Ruby
43 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/v0.46.1.tar.gz"
|
|
sha256 "492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231"
|
|
|
|
bottle do
|
|
cellar :any
|
|
sha256 "4c690ce6fff7b1fe564feffde0f2804eead80692a10af99ae568c880d0e7b748" => :catalina
|
|
sha256 "5ef9fc208160c101e37c01b74216ec48c9d6d53d16dffee4e434d4db36e378da" => :mojave
|
|
sha256 "199940d786f8092d549b3b66379a289966c37f51719c076d5c387dadbaeb1f81" => :high_sierra
|
|
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
|