From 35b81a0b85c877fe3a0b96bcd5b5f9dd75bb32f7 Mon Sep 17 00:00:00 2001 From: Yoshitaka Moriwaki Date: Sat, 2 Nov 2024 15:16:19 +0900 Subject: [PATCH] Remove temporarily 2 --- Formula/parsnp.rb | 65 ----------------------------------------------- Formula/phlawd.rb | 54 --------------------------------------- Formula/pirate.rb | 41 ------------------------------ Formula/roary.rb | 65 ----------------------------------------------- 4 files changed, 225 deletions(-) delete mode 100644 Formula/parsnp.rb delete mode 100644 Formula/phlawd.rb delete mode 100644 Formula/pirate.rb delete mode 100644 Formula/roary.rb diff --git a/Formula/parsnp.rb b/Formula/parsnp.rb deleted file mode 100644 index e432244a7..000000000 --- a/Formula/parsnp.rb +++ /dev/null @@ -1,65 +0,0 @@ -class Parsnp < Formula - # cite Treangen_2014: "https://doi.org/10.1186/s13059-014-0524-x" - desc "Microbial core genome alignment and SNP detection" - homepage "https://github.com/marbl/parsnp" - url "https://github.com/marbl/parsnp/archive/refs/tags/v2.0.5.tar.gz" - sha256 "1d23695d0d624fa17e02c43b1d730200e526c17a48615593f75ee8fc35402489" - head "https://github.com/marbl/parsnp.git", branch: "master" - - bottle do - root_url "https://ghcr.io/v2/brewsci/bio" - sha256 cellar: :any, arm64_sonoma: "d00efe0566c3c017d36630032599b252e5a19a78c01279fd8bbfba7abdf2045f" - sha256 cellar: :any, ventura: "6357c9eac4ac96eebaf8825cbb06eafcd26a30c0a0838b4e673889544683b9dc" - sha256 cellar: :any_skip_relocation, x86_64_linux: "36a5646f5c4c611c5e1b384541b06f490bb424f34a8e98439ab1e294a708b922" - end - - depends_on "autoconf" => :build - depends_on "automake" => :build - depends_on "libtool" => :build - depends_on "pkg-config" => :build - - depends_on "brewsci/bio/fasttree" - depends_on "brewsci/bio/harvest-tools" - - uses_from_macos "zlib" - - on_macos do - depends_on "libomp" - end - - def install - # remove binaries - rm Dir["bin/*"] - - # https://github.com/marbl/parsnp/issues/52 - inreplace "src/parsnp.cpp", "1.0.1", version.to_s - - cd "muscle" do - ENV.deparallelize - system "./autogen.sh" - system "./configure", "--prefix=#{prefix}" - system "make", "install" - (doc/"muscle").install "AUTHORS", "ChangeLog" - end - - system "./autogen.sh" - system "./configure", "--prefix=#{prefix}", "--with-libmuscle=#{include}" - - # https://github.com/marbl/parsnp/issues/57 - libr = " -lMUSCLE-3.7" - inreplace "src/Makefile", libr, "" - inreplace "src/Makefile", "LIBS =", "LIBS =#{libr}" - inreplace "src/Makefile", "LDFLAGS = ", "LDFLAGS = -L#{lib}" - - system "make" - - bin.install "src/parsnp_core" - bin.install_symlink "parsnp_core" => "parsnp" - pkgshare.install "examples" - doc.install "CITATION", "LICENSE", "README.md" - end - - test do - assert_match version.to_s, shell_output("#{bin}/parsnp -v 2>&1") - end -end diff --git a/Formula/phlawd.rb b/Formula/phlawd.rb deleted file mode 100644 index 9f61eb279..000000000 --- a/Formula/phlawd.rb +++ /dev/null @@ -1,54 +0,0 @@ -class Phlawd < Formula - # cite Smith_2009: "https://doi.org/10.1186/1471-2148-9-37" - desc "Phylogenetic dataset construction" - homepage "https://github.com/jonchang/phlawd" - url "https://github.com/jonchang/phlawd/archive/refs/tags/3.4b.tar.gz" - version "3.4b" - sha256 "a0fea43866e425f7fed5f74bcb8c391484a10b486f3f03d5b7bbc4df84dd84b8" - license "GPL-2.0" - revision 2 - - bottle do - root_url "https://ghcr.io/v2/brewsci/bio" - sha256 cellar: :any_skip_relocation, catalina: "ece6f29b1e9ae8f93d7e0cbf041f1bad949c68955f02ca9f0dbb0279d4b3d7b8" - sha256 cellar: :any_skip_relocation, x86_64_linux: "d93ccf2fdc9de7917a96a99c153983c8d8c5798b35a4e63ff247ab54fcdbb061" - end - - depends_on "brewsci/bio/muscle" - depends_on "brewsci/bio/quicktree" - depends_on "libomp" if OS.mac? - depends_on "mafft" - depends_on "wget" - - uses_from_macos "sqlite" - - def install - ENV.append_to_cflags "-mmacosx-version-min=10.12 -lomp" if OS.mac? - sql = OS.mac? ? "sqlitewrapped-1.3.1.MAC.tgz" : "sqlitewrapped-1.3.1.tar.gz" - - cd "deps" do - system "tar", "xf", sql, "--strip-components=1" - system "make" - end - - cd "src" do - inreplace "Makefile.in" do |s| - s.gsub! "fopenmp", "fopenmp @CFLAGS@" - s.gsub! "deps/$(HOST)", "deps" - end - - if OS.mac? - system "./configure", "ac_cv_prog_cxx_openmp=-Xpreprocessor -fopenmp" - else - system "./configure" - end - - system "make" - bin.install "PHLAWD" - end - end - - test do - assert_match version.to_s, shell_output("#{bin}/PHLAWD") - end -end diff --git a/Formula/pirate.rb b/Formula/pirate.rb deleted file mode 100644 index 35c384634..000000000 --- a/Formula/pirate.rb +++ /dev/null @@ -1,41 +0,0 @@ -class Pirate < Formula - # cite Bayliss_2019: "https://doi.org/10.1101/598391" - desc "Pangenome analysis and threshold evaluation toolbox" - homepage "https://github.com/SionBayliss/PIRATE" - url "https://github.com/SionBayliss/PIRATE/archive/refs/tags/v1.0.5.tar.gz" - sha256 "d5d7e657558eadae301a3198bccfd5ee04daddab1a872049d8a74cb71c35f20b" - license "GPL-3.0-or-later" - - bottle do - root_url "https://ghcr.io/v2/brewsci/bio" - sha256 cellar: :any_skip_relocation, arm64_sonoma: "f9c3d3f37065a05791b6c561888fbe9e3f532320a45c312018ae4130cd3fb853" - sha256 cellar: :any_skip_relocation, ventura: "f9c3d3f37065a05791b6c561888fbe9e3f532320a45c312018ae4130cd3fb853" - sha256 cellar: :any_skip_relocation, x86_64_linux: "2a810a4b27460809759ab9c9f2a62a4d58660b6281c9fd87a92b0cbc981c9883" - end - - depends_on "bioperl" - depends_on "blast" - depends_on "brewsci/bio/cd-hit" - depends_on "brewsci/bio/fasttree" - depends_on "brewsci/bio/mcl" - depends_on "diamond" - depends_on "mafft" - depends_on "parallel" - - uses_from_macos "perl" - uses_from_macos "unzip" - - def install - ENV.prepend "PERL5LIB", Formula["bioperl"].libexec/"lib/perl5" - libexec.install Dir["*"] - %w[PIRATE].each do |name| - (bin/name).write_env_script("#{libexec}/bin/#{name}", PERL5LIB: ENV["PERL5LIB"]) - end - end - - test do - assert_match version.to_s, shell_output("#{bin}/PIRATE --version 2>&1") - assert_match "pangenome", shell_output("#{bin}/PIRATE --help 2>&1") - system "#{bin}/PIRATE", "--check" - end -end diff --git a/Formula/roary.rb b/Formula/roary.rb deleted file mode 100644 index e34aad860..000000000 --- a/Formula/roary.rb +++ /dev/null @@ -1,65 +0,0 @@ -class Roary < Formula - # cite Page_2015: "https://doi.org/10.1093/bioinformatics/btv421" - desc "High speed stand alone pan-genome pipeline" - homepage "https://sanger-pathogens.github.io/Roary/" - url "https://github.com/sanger-pathogens/Roary/archive/refs/tags/v3.13.0.tar.gz" - sha256 "375f83c8750b0f4dea5b676471e73e94f3710bc3a327ec88b59f25eae1c3a1e8" - license "GPL-3.0-or-later" - - bottle do - root_url "https://ghcr.io/v2/brewsci/bio" - sha256 cellar: :any, arm64_sonoma: "40d2a5579b34f14be8d6fd91f544e4b7b532399a80f51709247e81403ce140ed" - sha256 cellar: :any, ventura: "d5dcd06d9a05405f1c2e64653e4396b76b72c09e078b8adfbd5cb2552ed33902" - sha256 cellar: :any_skip_relocation, x86_64_linux: "530c8a2fd8485a6346e3ff2d95d4fb5825facce7f5525db85385732d25639412" - end - - depends_on "cpanminus" => :build - depends_on "bedtools" - depends_on "bioperl" - depends_on "blast" - depends_on "brewsci/bio/cd-hit" - depends_on "brewsci/bio/fasttree" - depends_on "brewsci/bio/kraken" - depends_on "brewsci/bio/mcl" - depends_on "brewsci/bio/prank" - depends_on "mafft" - depends_on "openssl@3" - depends_on "parallel" - depends_on "perl" - - uses_from_macos "libxml2" - - def install - libexec.install Dir["bin/*"] - pkgshare.install "contrib" - - # let CPAN install these - rm_r buildpath/"lib" - rm_r buildpath/"t" - rm_r buildpath/"bin" - bin.mkpath - - ENV.prepend "PERL5LIB", Formula["perl"].libexec/"lib/perl5" - ENV.prepend_create_path "PERL5LIB", prefix/"perl5/lib/perl5" - - # --notest because https://github.com/sanger-pathogens/Roary/issues/386 - system "cpanm", "--notest", "--self-contained", "-l", prefix/"perl5", "Bio::Roary" - - Dir[libexec/"*"].each do |exe| - name = File.basename exe - (bin/name).write_env_script(exe, PERL5LIB: ENV["PERL5LIB"]) - end - end - - def caveats - <<~EOS - The included .R scripts need R and ggplot2 to be installed separately. - EOS - end - - test do - assert_match version.to_s, shell_output("#{bin}/roary -w 2>&1") - assert_match version.to_s, shell_output("#{bin}/roary -a 2>&1") - assert_match "core", shell_output("#{bin}/roary -h 2>&1") - end -end