.github/workflows/build-bottles.yml

@@ -8,46 +8,43 @@ env:
   HOMEBREW_NO_INSTALL_CLEANUP: 1
 
 jobs:
-  build-linux-bottles:
-    runs-on: ubuntu-latest
-    container:
-      image: homebrew/ubuntu16.04:master
-      options: --user root
-    steps:
-      - name: Update Homebrew
-        run: brew update-reset
-      - uses: actions/checkout@master
-      - name: Build bottles
-        run: |
-          mkdir -p "$(dirname $(brew --repo ${{github.repository}}))"
-          cp -a "$GITHUB_WORKSPACE" "$(brew --repo ${{github.repository}})"
-          mkdir ~/bottles
-          cd ~/bottles
-          brew test-bot --skip-recursive-dependents --root-url=https://ghcr.io/v2/brewsci/bio --git-name=Brewsci --git-email=linux@brew.sh
-          cp -a ~/bottles $RUNNER_TEMP/
-      - name: Upload bottles
-        uses: actions/upload-artifact@v1
-        with:
-          name: bottles
-          path: ${{runner.temp}}/bottles
-  build-macos-bottles:
-    runs-on: macos-10.15
+  build-bottles:
+    strategy:
+      matrix:
+        os: [ubuntu-18.04, macos-10.15]
+    runs-on: ${{ matrix.os }}
     env:
       HOMEBREW_FORCE_VENDOR_RUBY: 1
     steps:
-      - name: Update Homebrew
-        run: brew update-reset
-      - uses: actions/checkout@master
-      - name: Build bottles
-        run: |
-          mkdir -p "$(dirname $(brew --repo ${{github.repository}}))"
-          cp -a "$GITHUB_WORKSPACE" "$(brew --repo ${{github.repository}})"
-          mkdir ~/bottles
-          cd ~/bottles
-          brew test-bot --cleanup --root-url=https://ghcr.io/v2/brewsci/bio
-          cp -a ~/bottles $RUNNER_TEMP/
-      - name: Upload bottles
-        uses: actions/upload-artifact@v1
+      - name: Set up Homebrew
+        id: set-up-homebrew
+        uses: Homebrew/actions/setup-homebrew@master
+
+      - name: Cache Homebrew Bundler RubyGems
+        id: cache
+        uses: actions/cache@v1
+        with:
+          path: ${{ steps.set-up-homebrew.outputs.gems-path }}
+          key: ${{ runner.os }}-rubygems-${{ steps.set-up-homebrew.outputs.gems-hash }}
+          restore-keys: ${{ runner.os }}-rubygems-
+
+      - name: Install Homebrew Bundler RubyGems
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: brew install-bundler-gems
+
+      - run: brew test-bot --only-cleanup-before
+
+      - run: brew test-bot --only-setup
+
+      - run: brew test-bot --only-tap-syntax
+
+      - run: |
+          brew test-bot --only-formulae --only-json-tab --skip-recursive-dependents --root-url="https://ghcr.io/v2/brewsci/bio"
+        if: github.event_name == 'pull_request'
+
+      - name: Upload bottles as artifact
+        if: always() && github.event_name == 'pull_request'
+        uses: actions/upload-artifact@main
         with:
           name: bottles
-          path: ${{runner.temp}}/bottles
+          path: '*.bottle.*'

Formula/adam.rb

@@ -2,8 +2,8 @@ class Adam < Formula
   # cite Nothaft_2015: "https://doi.org/10.1145/2723372.2742787"
   desc "Genomics analysis platform built on Apache Avro, Apache Spark and Parquet"
   homepage "https://github.com/bigdatagenomics/adam"
-  url "https://search.maven.org/remotecontent?filepath=org/bdgenomics/adam/adam-distribution-spark3_2.12/0.36.0/adam-distribution-spark3_2.12-0.36.0-bin.tar.gz"
-  sha256 "870bba5906b9800261c1502010adbbeb5b592f589ea0279945b2f3f4beaa3cc5"
+  url "https://search.maven.org/remotecontent?filepath=org/bdgenomics/adam/adam-distribution-spark3_2.12/0.37.0/adam-distribution-spark3_2.12-0.37.0-bin.tar.gz"
+  sha256 "98800f24a154bd04fe19e7a8aa6c3f875005c5ff49b86b31d57c9cad75bec648"
 
   livecheck do
     url :homepage
@@ -13,8 +13,8 @@ class Adam < Formula
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any_skip_relocation, catalina:     "06e1b4022cedc5dac1f5d000591397bfaa48d28c2b5077f6c800da26834a34e6"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "ba384809ee683c40f4bfe1e08f8996d30f87dc5b34bd5ddd953df42a7a67c146"
+    sha256 cellar: :any_skip_relocation, catalina:     "cd1d89e3987bcf26e4ebfbb90f1b5c8f96c74260f2909fae335effdc38cf1b64"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "d78427a2817fbc0e4014d4d203cc5d410158a19ad13154f21001d6d83acd4953"
   end
 
   head do

Formula/andi.rb

@@ -2,14 +2,13 @@ class Andi < Formula
   # cite Hauboid_2015: "https://doi.org/10.1093/bioinformatics/btu815"
   desc "Estimate evolutionary distance between similar genomes"
   homepage "https://github.com/EvolBioInf/andi"
-  url "https://github.com/EvolBioInf/andi/archive/v0.13.tar.gz"
-  sha256 "3fb11f5399efdcbf98ecbbaa95b1a6cd98f887cf78554e460dc3f18d4880ae3e"
-  license "GPL-3.0"
+  url "https://github.com/EvolBioInf/andi/archive/v0.14.tar.gz"
+  sha256 "2c9e11524f38e74fe3f981e6acd9527c1a1ca30994a30c5e86808ba5165a25b7"
+  license "GPL-3.0-or-later"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any, catalina:     "78dcbf43bcb4cde0ba46cd02af556afceef520a7f04e998fea7d5b2910add590"
-    sha256 cellar: :any, x86_64_linux: "7ce8d573d03707e62060cb894e8b66779f1cd4190647d9ae0892cf0f87ceb580"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "c18b5df442cab486cfbbfb6d848f8fa6ea63ecf2468b9df5116e2faf4eff4698"
   end
 
   depends_on "autoconf" => :build

Formula/arcs.rb

@@ -2,14 +2,14 @@ class Arcs < Formula
   # cite Yeo_2017: "https://doi.org/10.1093/bioinformatics/btx675"
   desc "Scaffold genome sequence assemblies using linked or long reads"
   homepage "https://github.com/bcgsc/arcs"
-  url "https://github.com/bcgsc/arcs/releases/download/v1.2.2/arcs-1.2.2.tar.gz"
-  sha256 "9c3490eb77be198d28ca55eb10bae617f694f0abee0484d3f599e3354e97450b"
+  url "https://github.com/bcgsc/arcs/releases/download/v1.2.3/arcs-1.2.3.tar.gz"
+  sha256 "191c863e4fb556bdbad20e8dfa675cb35e209b9198ab06bb8e7b948d9469a066"
   license "GPL-3.0-only"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any,                 catalina:     "81a8593090662ffa6a3abd831591d4a20799e0352eca7fa8b96841e56542cb5e"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "c63717d8f1bac1db0b8bfff40e3433359c4df8f12add5805849e679ec99e0287"
+    sha256 cellar: :any,                 catalina:     "320d8b7397b75cbaeb3432f4ce1d887e411cb7c65d4930fa9eb120b69ce33ef9"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "3bd8cffcd05ac8c85e486b7c4f782c748de79df5d2feed438a82dc49cb25cf76"
   end
 
   head do

Formula/autodock-vina.rb

@@ -4,15 +4,15 @@ class AutodockVina < Formula
   include Language::Python::Virtualenv
   desc "Docking and virtual screening program"
   homepage "https://github.com/ccsb-scripps/AutoDock-Vina/"
-  url "https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.2.2.tar.gz"
-  sha256 "b9c28df478f90d64dbbb5f4a53972bddffffb017b7bb58581a1a0034fff1b400"
+  url "https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.2.3.tar.gz"
+  sha256 "22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0"
   license "Apache-2.0"
   head "https://github.com/ccsb-scripps/AutoDock-Vina.git", branch: "develop"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any,                 catalina:     "49a9ef97499d33d5607a5b247b3b7bb3ad4828b660bce873f081a0b69ec514a4"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "ebb375d43a962329c9a8b0f9e1a3540c66a60d0c3dd546ea6d3088fee7e7aec7"
+    sha256 cellar: :any,                 catalina:     "34c63eafaa1fed7aa322060b2e7f4226a9807ea5ab138e1c3d36c364a3c1eddf"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "752706c4bfde2ce4f437b0eaa6be4f10e6da801b2f771fe8d904c6c51a90266b"
   end
 
   depends_on "swig" => :build

Formula/bali-phy.rb

@@ -3,10 +3,10 @@ class BaliPhy < Formula
   # cite Redelings_2014: "https://dx.doi.org/10.1093/molbev/msu174"
   desc "Bayesian co-estimation of phylogenies and multiple alignments"
   homepage "http://www.bali-phy.org/"
-  url "https://github.com/bredelings/BAli-Phy/archive/3.6.0.tar.gz"
-  sha256 "88f1922f80d0376ec2a0929d72d69258eac3dfba0eef13aab3f9c460db1ac0b6"
+  url "https://github.com/bredelings/BAli-Phy/archive/3.6.1.tar.gz"
+  sha256 "6591f39d5708f5c34fca244f20326c6cba30bb32c80b72c6ae2e7e23bafcf11a"
   license "GPL-2.0-or-later"
-  head "https://github.com/bredelings/BAli-Phy.git"
+  head "https://github.com/bredelings/BAli-Phy.git", branch: "master"
 
   livecheck do
     url :stable
@@ -15,8 +15,8 @@ class BaliPhy < Formula
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any,                 catalina:     "272d54b06c0906e3fe6041c156d6fb748d0f2c27ff1c32d4271543fb302368a6"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "4d1dd23a90021c9a833c0d7a51a454481eb862acfd832e7f53be5eeea5a36f1b"
+    sha256 cellar: :any,                 catalina:     "be42fc5e484110a6ad5379ca889cb213788f647af30c0531945bd48d363c5355"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "fe3b2a4ac7350c0172be7d30f67c7a742d6545c5e266a4ff9cf6290afa0a160d"
   end
 
   depends_on "meson" => :build

Formula/bowtie.rb

@@ -4,8 +4,8 @@ class Bowtie < Formula
   # cite Langmead_2009: "https://doi.org/10.1186/gb-2009-10-3-r25"
   desc "Ultrafast memory-efficient short read aligner"
   homepage "https://bowtie-bio.sourceforge.io/"
-  url "https://github.com/BenLangmead/bowtie/archive/v1.3.0.tar.gz"
-  sha256 "d7c2d982a67884909f284a0ff150b56b20127cd7a1ced461c3c4c03e6a6374c5"
+  url "https://github.com/BenLangmead/bowtie/archive/refs/tags/v1.3.1.tar.gz"
+  sha256 "147d9fe9652f7c5f351bfc0eb012e06981986fb43bd6bdfe88a95c02eabc6573"
   license "Artistic-2.0"
   head "https://github.com/BenLangmead/bowtie.git"
 
@@ -16,8 +16,8 @@ class Bowtie < Formula
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any_skip_relocation, catalina:     "097544d5656a7fab72b8d36e08bc7e2be4032fdd573fa205ad4da9ad5d7bf56a"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "cf888db0331e61e96ebc6ea51418af5a1f9045d83c49c560d65cb396a448ac4d"
+    sha256 cellar: :any_skip_relocation, catalina:     "42de0f90a500103a2736bf4728d267a0e729096bc8ce45b6d3ef9a21cd86d87d"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "a4bd1d75bc2a132f22122093a993a53c174a3a80045df118016b58dbdca4a869"
   end
 
   depends_on "python"

Formula/breseq.rb

@@ -2,8 +2,8 @@ class Breseq < Formula
   # Deatherage_2014: "https://doi.org/10.1007/978-1-4939-0554-6_12"
   desc "Find mutations in microbes from short reads"
   homepage "https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing"
-  url "https://github.com/barricklab/breseq/releases/download/v0.35.4/breseq-0.35.4-Source.tar.gz"
-  sha256 "762f7b6aac26bddb5a39724e103267bd48d597d74fa7a8006d2bf0bd68fe86b4"
+  url "https://github.com/barricklab/breseq/releases/download/v0.36.1/breseq-0.36.1.Source.tar.gz"
+  sha256 "d8904de452366237f9727fe4b025578de158da808cd41de9de042f2ba9233562"
   head "https://github.com/barricklab/breseq.git"
 
   bottle do

Formula/cannoli.rb

@@ -1,8 +1,8 @@
 class Cannoli < Formula
   desc "Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools"
   homepage "https://github.com/bigdatagenomics/cannoli"
-  url "https://search.maven.org/remotecontent?filepath=org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.14.0/cannoli-distribution-spark3_2.12-0.14.0-bin.tar.gz"
-  sha256 "c64b0b1c47b5d996ed99f95e92f289d7268256da9f49079c88b10d21d0a4b5ad"
+  url "https://search.maven.org/remotecontent?filepath=org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.15.0/cannoli-distribution-spark3_2.12-0.15.0-bin.tar.gz"
+  sha256 "a92cdedc72066e8e022bbe6a6aaf092bd24fa25c839212a34f5a1371f9744a78"
 
   livecheck do
     url :homepage
@@ -12,8 +12,8 @@ class Cannoli < Formula
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any_skip_relocation, catalina:     "23fe1316373ee3c3f0535f5828d9f3571769b2c4f81e18c59cc2c70065741783"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "9fbdacbf448f1f67de4051206e6421914488f4ebb3ff275b38c16c678d705478"
+    sha256 cellar: :any_skip_relocation, catalina:     "2fc56aaf33a0603f81e264a19ddf2cb5e46b6e21b2779b65c2d4929491d1d7c6"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "a001cf63e829cbb5abc956d6f50ca7fc4203c4e2e0dfeb17e1e926c20817410d"
   end
 
   head do

Formula/clipper4coot.rb

@@ -1,25 +1,23 @@
 class Clipper4coot < Formula
   desc "Crystallographic automation and complex data manipulation libraries"
-  homepage "https://www2.mrc-lmb.cam.ac.uk/"
+  homepage "https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies"
   url "https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-2.1.20180802.tar.gz"
   sha256 "7c7774f224b59458e0faa104d209da906c129523fa737e81eb3b99ec772b81e0"
   license "LGPL-2.1-only"
-  revision 1
+  revision 2
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any,                 catalina:     "b59b536495ee9b1691296458c4f0125c68c76de5e729738430621504492e1896"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "ce93bf961cd711153db05d726dbc9a0662c1e2d0d7af075ec99bb95015f71f43"
+    sha256 cellar: :any,                 catalina:     "59a95fd391ef958374698000125b2bea0577ceb2d99f6af9f6f1f3ea05ae4a68"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "45f6f41305ce655b0e8517b2fb03e180f03c9f85d5553317f1b0b0eea6fbf8fc"
   end
 
-  depends_on "binutils" => :build
   depends_on "pkg-config" => [:build, :test]
   depends_on "brewsci/bio/libccp4"
   depends_on "brewsci/bio/mmdb2"
-  depends_on "glib"
 
   resource "libfftw2" do
-    url "http://www.fftw.org/fftw-2.1.5.tar.gz"
+    url "https://fftw.org/fftw-2.1.5.tar.gz"
     sha256 "f8057fae1c7df8b99116783ef3e94a6a44518d49c72e2e630c24b689c6022630"
   end
 
@@ -42,9 +40,13 @@ def install
         "--enable-float",
         "--disable-static",
       ]
-      simd_args = []
-      simd_args << "--enable-sse2" << "--enable-avx" if Hardware::CPU.intel?
-      system "./configure", *(args + simd_args)
+      # Hack for M1 Mac (https://github.com/pemsley/coot/issues/33#issuecomment-1086907650)
+      if Hardware::CPU.arm? && OS.mac?
+        args << "--build=arm-apple-#{OS.kernel_name.downcase}#{OS.kernel_version.major}"
+      end
+      # Avoid -flat_namespace usage on macOS
+      inreplace "./configure", "-flat_namespace -undefined suppress", "-undefined dynamic_lookup" if OS.mac?
+      system "./configure", *args
       system "make", "install"
     end
 

Formula/dsh-bio.rb

@@ -1,14 +1,14 @@
 class DshBio < Formula
   desc "Tools for BED, FASTA, FASTQ, GAF, GFA1/2, GFF3, PAF, SAM, and VCF files"
   homepage "https://github.com/heuermh/dishevelled-bio"
-  url "https://search.maven.org/remotecontent?filepath=org/dishevelled/dsh-bio-tools/2.0.6/dsh-bio-tools-2.0.6-bin.tar.gz"
-  sha256 "331afe5f1804a20a3c24dd00ed4597c3dc380257265d86afe3ca8d46188884d9"
+  url "https://search.maven.org/remotecontent?filepath=org/dishevelled/dsh-bio-tools/2.0.8/dsh-bio-tools-2.0.8-bin.tar.gz"
+  sha256 "916f76fb0667aca55259deaba95df1f6ac132a538eca72358c922ea02562b26c"
   license "LGPL-3.0-or-later"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any_skip_relocation, catalina:     "c17fdd3a27c571770a54b2c1e8d99bf1794bd6545e43b771983f8b9b2f01f48c"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "e25b8ea4afd9243d4fa20fb2fb55e02393aff042348c65c14f67b5a317aac43c"
+    sha256 cellar: :any_skip_relocation, catalina:     "3aff2dd93a8e2a49dc2cf79749f2017e01af87c1f141a5b213eade33b90bd756"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "9cdee00ca6ea213a544813a588a4433660f807749e9c164ea2031638b452198b"
   end
 
   depends_on "openjdk"

Formula/gemmi.rb

@@ -1,15 +1,15 @@
 class Gemmi < Formula
   desc "Macromolecular crystallography library and utilities"
   homepage "https://project-gemmi.github.io/"
-  url "https://github.com/project-gemmi/gemmi/archive/refs/tags/v0.5.1.tar.gz"
-  sha256 "75669168342ba6e2251ed592f9714600bc0edabd9c4faefdc004d94ff41e6eb4"
+  url "https://github.com/project-gemmi/gemmi/archive/refs/tags/v0.5.3.tar.gz"
+  sha256 "c58dde34751a27aca30dabdf925a79dd179093ed1b1952172a116bbd12a350b9"
   license "MPL-2.0"
   head "https://github.com/project-gemmi/gemmi.git", branch: "master"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any_skip_relocation, catalina:     "3676d5b56a21b80d744f875a8dc7fca1da342a4f617d447aa481891890960a71"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "3866f4a81a539f0a09b044ecea211c8951a83444906d3c2ce303266beff6ac62"
+    sha256 cellar: :any_skip_relocation, catalina:     "0d61b3b9d065e2aa1cc404f0656ecad79db74970b4d1ca937c2842fcf5b1e024"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "e12d0fc99ceabf787593b472d94cd5bc791f22818aefe9784e17669e483839f2"
   end
 
   depends_on "cmake" => :build

Formula/jmol.rb

@@ -1,14 +1,14 @@
 class Jmol < Formula
   desc "Open-source Java viewer for chemical structures in 3D"
   homepage "https://jmol.sourceforge.io/"
-  url "https://downloads.sourceforge.net/project/jmol/Jmol/Version%2014.32/Jmol%2014.32.10/Jmol-14.32.10-binary.zip"
-  sha256 "a7d0d1f16dcd740108eb1bb4c653cd31597085cd616455463fc22cb85f12e74e"
+  url "https://downloads.sourceforge.net/project/jmol/Jmol/Version%2014.32/Jmol%2014.32.46/Jmol-14.32.46-binary.zip"
+  sha256 "20a0001b2933113794d2af8d64d3b053f494a0356b47dc3a3ede9c5ed6a832df"
   license "LGPL-2.1-or-later"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any_skip_relocation, catalina:     "fbbb8c9d82d2d3c750f25b99bcac0ece1eb7c498c286fb88f6cc04bd09f5f79a"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "c7cb98b8a2cddebfd80becde27d315a326fe26e9d05cd2951485bb41277cfcfc"
+    sha256 cellar: :any_skip_relocation, catalina:     "ccfdead4dcb16171e37618c42d74d33c1eb1db09272706e425dbeb3fc56b50eb"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "99580c3fd53aa41c25a6a5c971c22ca31fe852e6b0f875958578050501cfe157"
   end
 
   head do
@@ -36,16 +36,12 @@ def install
   end
 
   test do
-    on_macos do
-      assert_match version.to_s, shell_output("#{bin}/jmol -n")
-    end
+    assert_match version.to_s, shell_output("#{bin}/jmol -n") if OS.mac?
 
-    on_linux do
+    if OS.linux? && ENV["HOMEBREW_GITHUB_ACTIONS"]
       # unfortunately, the application can not be run headless
-      if ENV["HOMEBREW_GITHUB_ACTIONS"]
-        assert_match "java.awt.HeadlessException",
+      assert_match "java.awt.HeadlessException",
 shell_output("#{bin}/jmol -n 2>&1", 1)
-      end
     end
   end
 end

Formula/kalign.rb

@@ -2,14 +2,14 @@ class Kalign < Formula
   # cite Lassmann_2019: "https://doi.org/10.1093/bioinformatics/btz795"
   desc "SIMD accelerated multiple sequence alignment"
   homepage "https://github.com/TimoLassmann/kalign"
-  url "https://github.com/TimoLassmann/kalign/archive/v3.3.1.tar.gz"
-  sha256 "7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390"
+  url "https://github.com/TimoLassmann/kalign/archive/v3.3.2.tar.gz"
+  sha256 "c0b357feda32e16041cf286a4e67626a52bbf78c39e2237b485d54fb38ef319a"
   license "GPL-3.0"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
-    sha256 cellar: :any_skip_relocation, catalina:     "176d55fb00ad9c6497048b311525948747f475ed1a20ec14b82c465061deeaec"
-    sha256 cellar: :any_skip_relocation, x86_64_linux: "0296db9227e230d5e65e5f3d044fec6dfcac288a8f10fc29a18dd3a1f4b68245"
+    sha256 cellar: :any_skip_relocation, catalina:     "7cce83abecd04993bb30ae4b898346b6dd22efd471cd52559d34da61400e6dec"
+    sha256 cellar: :any_skip_relocation, x86_64_linux: "df20a7be2f77b47aa2fe2e01dbfb974cba84be92ddbc9b4ec6d18a01594d3e62"
   end
 
   depends_on "autoconf" => :build