qtltools 1.3.1 (new formula) (#1823)

Formula/qtltools.rb

@@ -0,0 +1,63 @@
+class Qtltools < Formula
+  # cite Delaneau_2017: "https://doi.org/10.1038/ncomms15452"
+  # cite Ongen_2017: "https://doi.org/10.1038/ng.3981"
+  # cite Fort_2017: "https://doi.org/10.1093/bioinformatics/btx074"
+  desc "Complete tool set for molecular QTL discovery and analysis"
+  homepage "https://qtltools.github.io/qtltools/"
+  url "https://github.com/qtltools/qtltools/archive/refs/tags/1.3.1.tar.gz"
+  sha256 "033b9b61923fd65c4b8b80bc0add321e6fd6fb40de49d15c2dfe6a4d7e60764a"
+  license "GPL-3.0-or-later"
+  head "https://github.com/qtltools/qtltools.git", branch: "master"
+
+  depends_on "pkg-config" => :build
+  depends_on "boost"
+  depends_on "gsl"
+  depends_on "htslib"
+  depends_on "libdeflate"
+  depends_on "openssl@3"
+  depends_on "pcre2"
+  depends_on "r"
+  depends_on "xz" # for lzma
+
+  uses_from_macos "bzip2"
+  uses_from_macos "curl"
+  uses_from_macos "zlib"
+
+  def install
+    inreplace "Makefile" do |s|
+      s.gsub! "prefix      = /usr/local", "prefix = #{prefix}"
+      s.gsub! "autocompdir = /usr/local/etc/bash_completion.d", "autocompdir = #{prefix}/etc/bash_completion.d"
+      s.gsub! "autocompdir = /etc/bash_completion.d", "autocompdir = #{prefix}/etc/bash_completion.d"
+    end
+    args = [
+      "BOOST_INC=#{Formula["boost"].opt_include}",
+      "BOOST_LIB=#{Formula["boost"].opt_lib}",
+      "RMATH_INC=#{Formula["r"].opt_include}",
+      "RMATH_LIB=#{Formula["r"].opt_lib}",
+      "HTSLD_INC=#{Formula["htslib"].opt_include}",
+      "HTSLD_LIB=#{Formula["htslib"].opt_lib}",
+      "LIB_FLAGS=-lz -lgsl -lbz2 -llzma -lgslcblas -lm -lpthread -lcurl -lhts -ldeflate -lssl -lcrypto",
+    ]
+    system "make", *args
+    system "make", "install"
+  end
+
+  test do
+    resource "testdata" do
+      url "https://github.com/qtltools/qtltools/raw/master/example_files/genes.50percent.chr22.bed.gz"
+      sha256 "fc50a0750194971d18ba28ac69f787ba10c26bd03eb204ef1cd88b3d22b28d7d"
+    end
+    resource "testdata_index" do
+      url "https://github.com/qtltools/qtltools/raw/master/example_files/genes.50percent.chr22.bed.gz.tbi"
+      sha256 "dbbde52b174e6e702142aa2b7118e161ba48b11f2d2f3ef7a87307203e6d4602"
+    end
+    resource("testdata").fetch
+    cp resource("testdata").cached_download, testpath/"genes.50percent.chr22.bed.gz"
+    resource("testdata_index").fetch
+    cp resource("testdata_index").cached_download, testpath/"genes.50percent.chr22.bed.gz.tbi"
+    system "#{bin}/QTLtools", "pca", "--bed", "genes.50percent.chr22.bed.gz", "--scale",
+          "--center", "--out", "genes.50percent.chr22"
+    assert_predicate testpath/"genes.50percent.chr22.pca_stats", :exist?
+    assert_match "prop_var", File.read("genes.50percent.chr22.pca_stats")
+  end
+end