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mummer 3.23 #1830

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YoshitakaMo wants to merge 4 commits into develop from mummer

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Formula/circlator.rb

-Original file line number
+Diff line change
@@ -1,13 +1,11 @@
     class Circlator < Formula
       # cite Hunt_2015: "https://doi.org/10.1186/s13059-015-0849-0"
       include Language::Python::Virtualenv
       desc "Tool to circularize genome assemblies"
       homepage "https://sanger-pathogens.github.io/circlator/"
       url "https://github.com/sanger-pathogens/circlator/archive/refs/tags/v1.5.5.tar.gz"
       sha256 "927b6c156bfba6fa02db0c1173e280f85373320814c51e084170df583e604a2a"
-      license "GPL-3.0"
+      license "GPL-3.0-or-later"
       livecheck do
         url :stable
@@ Expand All / @@ -22,10 +20,10 @@ @@
       end
       depends_on arch: :x86_64 # spades is not supported on ARM
-      depends_on "brewsci/bio/mummer"
       depends_on "bwa"
+      depends_on "openssl@3"
       depends_on "prodigal"
-      depends_on "python"
+      depends_on "python@3.12"
       depends_on "samtools"
       depends_on "spades"
@@ Expand Down Expand Up / @@ -66,12 +64,12 @@ @@
         sha256 "b169ffbe0efb39fd193779e5982da1de86e392dfe66c6bc49d79aa34fe58b46b"
       end
       def install
         virtualenv_install_with_resources
       end
       test do
-        ENV.prepend_path "PATH", Formula["python"].opt_libexec/"bin"
+        ENV.prepend_path "PATH", Formula["python@3.12"].opt_libexec/"bin"
         output = shell_output("#{bin}/circlator test outdir")
         assert_match "Finished run on test data OK", output
       end
@@ Expand Down @@

Formula/iva.rb

-Original file line number
+Diff line change
@@ -1,4 +1,4 @@
     class Iva < Formula
       include Language::Python::Virtualenv
       # cite Hunt_2015: "https://doi.org/10.1093/bioinformatics/btv120"
@@ Expand All / @@ -15,11 +15,10 @@ @@
       end
       depends_on "brewsci/bio/kmc"
-      depends_on "brewsci/bio/mummer"
       depends_on "brewsci/bio/smalt"
       depends_on "libdeflate"
       depends_on "numpy"
-      depends_on "python@3.10"
+      depends_on "python@3.12"
       depends_on "samtools"
       resource "cython" do
@@ Expand Down Expand Up / @@ -52,7 +51,7 @@ @@
         sha256 "dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb"
       end
       def install
         virtualenv_install_with_resources
       end
@@ Expand Down @@

Formula/mummer.rb

-Original file line number
+Diff line change
@@ Expand Up / @@ -12,7 +12,9 @@ class Mummer < Formula @@
         sha256 cellar: :any_skip_relocation, x86_64_linux: "22df96cb1a3e421e5af2e432e3cfc10834ee13fa1e2916aae6a820dbcddcf8c5"
       end
-      depends_on "tcsh" unless OS.mac?
+      depends_on "openssl@3"
+      depends_on "tcsh"
+      uses_from_macos "perl"
       # Fix the error: Can't use 'defined(%hash)'
       patch do
@@ Expand Down @@

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