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ntsynt 1.0.8 #2293

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bd0159d
ntsynt 1.0.8
BenjaminDEMAILLE Jul 7, 2026
9a835ad
ntsynt: pin setuptools resource to fix pybedtools build
BenjaminDEMAILLE Jul 10, 2026
d7b4fef
ntsynt: build pybedtools without build isolation
BenjaminDEMAILLE Jul 11, 2026
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16 changes: 13 additions & 3 deletions Formula/ntsynt.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,8 @@
desc "Detecting multi-genome synteny using minimizer graph mapping"
homepage "https://github.com/bcgsc/ntSynt"
url "https://github.com/bcgsc/ntSynt.git",
tag: "v1.0.2",
revision: "f7e358fb1b58e7a1c33f3a876a29214e185c5dde"
tag: "v1.0.8",
revision: "ffef728f16334af9aef15338de97014e3494f83f"
license "GPL-3.0-or-later"
head "https://github.com/bcgsc/ntSynt.git", branch: "main"

Expand Down Expand Up @@ -242,6 +242,11 @@
sha256 "d72a210824facfdaf8768cf2d7ca25a042c30320b3020de2fa04640920d4e121"
end

resource "setuptools" do
url "https://files.pythonhosted.org/packages/0d/1c/73e719955c59b8e424d015ab450f51c0af856ae46ea2da83eba51cc88de1/setuptools-81.0.0.tar.gz"
sha256 "487b53915f52501f0a79ccfd0c02c165ffe06631443a886740b91af4b7a5845a"
end

resource "smart-open" do
url "https://files.pythonhosted.org/packages/06/84/c6e6276a72a78996f11118b8bc1d9e9b619aa78201f408210f4a584bd377/smart_open-7.0.4.tar.gz"
sha256 "62b65852bdd1d1d516839fcb1f6bc50cd0f16e05b4ec44b52f43d38bcb838524"
Expand Down Expand Up @@ -331,9 +336,14 @@
which("python3.12")
end

def install

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GitHub Actions / build-bottles (macos-15)

`brew install --verbose --formula --build-bottle brewsci/bio/ntsynt` failed on macOS Sequoia (15) on Apple Silicon! 

      fout.write(asset.get_content())
                 ^^^^^^^^^^^^^^^^^^^
    File "/private/tmp/ntsynt--snakemake-20260711-51221-h92s5d/snakemake-8.19.0/snakemake/assets/__init__.py", line 29, in get_content
      raise AssetDownloadError(
  assets.AssetDownloadError: Checksum mismatch when downloading asset https://cdn.tailwindcss.com/3.0.23?plugins=forms@0.4.0,typography@0.5.2
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> No available output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /opt/homebrew/Cellar/ntsynt/1.0.8/libexec/bin/python /opt/homebrew/Cellar/python@3.12/3.12.13_4/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py get_requires_for_build_wheel /private/tmp/tmpwm160648
  cwd: /private/tmp/ntsynt--snakemake-20260711-51221-h92s5d/snakemake-8.19.0
  Getting requirements to build wheel: finished with status 'error'
ERROR: Failed to build 'file:///private/tmp/ntsynt--snakemake-20260711-51221-h92s5d/snakemake-8.19.0' when getting requirements to build wheel

==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/ntsynt.rb
==> Configuration
HOMEBREW_VERSION: 6.0.9-112-g34c40c1
ORIGIN: https://github.com/Homebrew/brew
HEAD: 34c40c18ffa2029b611b61c73273e32c003d0842
Last commit: 4 hours ago
Branch: main
Core tap HEAD: 79617831ec01b4c19e6950096680e1161600ce42
Core tap last commit: 6 days ago
Core tap JSON: 11 Jul 19:39 UTC
Core cask tap HEAD: ab91e1260a8756649b1f8a9e1c13e4d5a408c3be
Core cask tap last commit: 6 days ago
Core cask tap JSON: 11 Jul 19:39 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CACHE: /Users/runner/Library/Caches/Homebrew
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_COLOR: set
HOMEBREW_CURL_PATH: /usr/bin/curl
HOMEBREW_DOWNLOAD_CONCURRENCY: 6
HOMEBREW_FAIL_LOG_LINES: 150
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_GIT_EMAIL: 1589480+BrewTestBot@users.noreply.github.com
HOMEBREW_GIT_NAME: BrewTestBot
HOMEBREW_GIT_PATH: /usr/bin/git
HOMEBREW_LOGS: /Users/runner/work/homebrew-bio/homebrew-bio/logs
HOMEBREW_MAKE_JOBS: 3
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_EMOJI: set
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_REQUIRE_TAP_TRUST: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 4.0.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/4.0.5_1/bin/ruby
CPU: 3-core 64-bit dunno
Clang: 17.0.0 build 1700
Git: 2.39.5 => /usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 15.7.7-arm64
CLT: 16.4.0.0.1.1747106510
Xcode: 16.4 => /Applications/Xcode_16.4.app/Contents/Developer
Rosetta 2: false
==> ENV
HOMEBREW_CC: clang
MAKEFLAGS: -j3
CMAKE_PREFIX_PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:/opt/homebrew/opt/libomp:/opt/homebrew/opt/openblas:/opt/homebrew/opt/readline:/opt/homebrew/opt/sqlite:/opt/homebrew/opt/cython:/opt/homebrew
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX15.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX15.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH: /opt/homebrew/opt/python@3.14/Frameworks:/opt/homebrew/opt/python@3.12/Frameworks
PKG_CONFIG_PATH: /opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/gmp/lib/pkgconfig:/opt/homebrew/opt/isl/lib/pkgconfig:/opt/homebrew/opt/mpfr/lib/pkgconfig:/opt/homebrew/opt/libmpc/lib/pkgconfig:/opt/homebrew/opt/lz4/lib/pkgconfig:/opt/homebrew/opt/zstd/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/opt/coinutils/lib/pkgconfig:/opt/homebrew/opt/osi/lib/pkgconfig:/opt/homebrew/opt/clp/lib/pkgconfig:/opt/homebrew/opt/cgl/lib/pkgconfig:/opt/homebrew/opt/cbc/lib/pkgconfig:/opt/homebrew/opt/mpdecimal/lib/pkgconfig:/opt/homebrew/opt/openssl@3/lib/pkgconfig:/opt/homebrew/

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`brew install --verbose --formula --build-bottle brewsci/bio/ntsynt` failed on macOS Tahoe (26) on Apple Silicon! 

      fout.write(asset.get_content())
                 ^^^^^^^^^^^^^^^^^^^
    File "/private/tmp/ntsynt--snakemake-20260711-48420-wksx5y/snakemake-8.19.0/snakemake/assets/__init__.py", line 29, in get_content
      raise AssetDownloadError(
  assets.AssetDownloadError: Checksum mismatch when downloading asset https://cdn.tailwindcss.com/3.0.23?plugins=forms@0.4.0,typography@0.5.2
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> No available output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /opt/homebrew/Cellar/ntsynt/1.0.8/libexec/bin/python /opt/homebrew/Cellar/python@3.12/3.12.13_4/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py get_requires_for_build_wheel /private/tmp/tmpgfklg1z2
  cwd: /private/tmp/ntsynt--snakemake-20260711-48420-wksx5y/snakemake-8.19.0
  Getting requirements to build wheel: finished with status 'error'
ERROR: Failed to build 'file:///private/tmp/ntsynt--snakemake-20260711-48420-wksx5y/snakemake-8.19.0' when getting requirements to build wheel

==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/ntsynt.rb
==> Configuration
HOMEBREW_VERSION: 6.0.9-112-g34c40c1
ORIGIN: https://github.com/Homebrew/brew
HEAD: 34c40c18ffa2029b611b61c73273e32c003d0842
Last commit: 5 hours ago
Branch: main
Core tap HEAD: 907454ea24f451d2a462f6c364099277a553b866
Core tap last commit: 12 days ago
Core tap JSON: 11 Jul 20:00 UTC
Core cask tap HEAD: f5bbf0c10c7ca19568f0b4422352990b1c6dfdef
Core cask tap last commit: 12 days ago
Core cask tap JSON: 11 Jul 20:00 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CACHE: /Users/runner/Library/Caches/Homebrew
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_COLOR: set
HOMEBREW_CURL_PATH: /usr/bin/curl
HOMEBREW_DOWNLOAD_CONCURRENCY: 6
HOMEBREW_FAIL_LOG_LINES: 150
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_GIT_EMAIL: 1589480+BrewTestBot@users.noreply.github.com
HOMEBREW_GIT_NAME: BrewTestBot
HOMEBREW_GIT_PATH: /usr/bin/git
HOMEBREW_LOGS: /Users/runner/work/homebrew-bio/homebrew-bio/logs
HOMEBREW_MAKE_JOBS: 3
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_EMOJI: set
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_REQUIRE_TAP_TRUST: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 4.0.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/4.0.5_1/bin/ruby
CPU: 3-core 64-bit dunno
Clang: 21.0.0 build 2100
Git: 2.50.1 => /usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.4-arm64
CLT: 26.6.0.0.1781586589
Xcode: 26.5 => /Applications/Xcode_26.5.app/Contents/Developer
Metal Toolchain: 17.0 (17F42)
Rosetta 2: false
==> ENV
HOMEBREW_CC: clang
MAKEFLAGS: -j3
CMAKE_PREFIX_PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:/opt/homebrew/opt/libomp:/opt/homebrew/opt/openblas:/opt/homebrew/opt/readline:/opt/homebrew/opt/sqlite:/opt/homebrew/opt/cython:/opt/homebrew
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH: /opt/homebrew/opt/python@3.14/Frameworks:/opt/homebrew/opt/python@3.12/Frameworks
PKG_CONFIG_PATH: /opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/gmp/lib/pkgconfig:/opt/homebrew/opt/isl/lib/pkgconfig:/opt/homebrew/opt/mpfr/lib/pkgconfig:/opt/homebrew/opt/libmpc/lib/pkgconfig:/opt/homebrew/opt/lz4/lib/pkgconfig:/opt/homebrew/opt/zstd/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/opt/coinutils/lib/pkgconfig:/opt/homebrew/opt/osi/lib/pkgconfig:/opt/homebrew/opt/clp/lib/pkgconfig:/opt/homebrew/opt/cgl/lib/pkgconfig:/opt/homebrew/opt/cbc/lib/pkgconfig:/opt/homebrew/opt/mpdecimal/lib/pkgconfig:/opt/homebrew/opt/openssl@3/

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`brew install --verbose --formula --build-bottle brewsci/bio/ntsynt` failed on macOS Sonoma (14) on Apple Silicon! 

      fout.write(asset.get_content())
                 ^^^^^^^^^^^^^^^^^^^
    File "/private/tmp/ntsynt--snakemake-20260711-25302-5le8r1/snakemake-8.19.0/snakemake/assets/__init__.py", line 29, in get_content
      raise AssetDownloadError(
  assets.AssetDownloadError: Checksum mismatch when downloading asset https://cdn.tailwindcss.com/3.0.23?plugins=forms@0.4.0,typography@0.5.2
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> No available output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /opt/homebrew/Cellar/ntsynt/1.0.8/libexec/bin/python /opt/homebrew/Cellar/python@3.12/3.12.13_4/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py get_requires_for_build_wheel /private/tmp/tmpv60skvrt
  cwd: /private/tmp/ntsynt--snakemake-20260711-25302-5le8r1/snakemake-8.19.0
  Getting requirements to build wheel: finished with status 'error'
ERROR: Failed to build 'file:///private/tmp/ntsynt--snakemake-20260711-25302-5le8r1/snakemake-8.19.0' when getting requirements to build wheel

==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/ntsynt.rb
==> Configuration
HOMEBREW_VERSION: 6.0.9-112-g34c40c1
ORIGIN: https://github.com/Homebrew/brew
HEAD: 34c40c18ffa2029b611b61c73273e32c003d0842
Last commit: 5 hours ago
Branch: main
Core tap HEAD: c1fb51517a40990c55bc1abbac13d856567fa9cc
Core tap last commit: 13 days ago
Core tap JSON: 11 Jul 20:19 UTC
Core cask tap HEAD: 0ff252f7ba2c1d369265bdddbf48b7f2c7dd3eff
Core cask tap last commit: 13 days ago
Core cask tap JSON: 11 Jul 20:19 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CACHE: /Users/runner/Library/Caches/Homebrew
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_COLOR: set
HOMEBREW_CURL_PATH: /usr/bin/curl
HOMEBREW_DOWNLOAD_CONCURRENCY: 6
HOMEBREW_FAIL_LOG_LINES: 150
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_GIT_EMAIL: 1589480+BrewTestBot@users.noreply.github.com
HOMEBREW_GIT_NAME: BrewTestBot
HOMEBREW_GIT_PATH: /usr/bin/git
HOMEBREW_LOGS: /Users/runner/work/homebrew-bio/homebrew-bio/logs
HOMEBREW_MAKE_JOBS: 3
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_EMOJI: set
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_REQUIRE_TAP_TRUST: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 4.0.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/4.0.5_1/bin/ruby
CPU: 3-core 64-bit dunno
Clang: 15.0.0 build 1500
Git: 2.39.3 => /usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 14.8.7-arm64
CLT: 16.2.0.0.1.1733547573
Xcode: 15.4 => /Applications/Xcode_15.4.app/Contents/Developer
Rosetta 2: false
==> ENV
HOMEBREW_CC: clang
MAKEFLAGS: -j3
CMAKE_PREFIX_PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:/opt/homebrew/opt/libomp:/opt/homebrew/opt/openblas:/opt/homebrew/opt/readline:/opt/homebrew/opt/sqlite:/opt/homebrew/opt/expat:/opt/homebrew/opt/cython:/opt/homebrew
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH: /opt/homebrew/opt/python@3.14/Frameworks:/opt/homebrew/opt/python@3.12/Frameworks
PKG_CONFIG_PATH: /opt/homebrew/opt/xz/lib/pkgconfig:/opt/homebrew/opt/gmp/lib/pkgconfig:/opt/homebrew/opt/isl/lib/pkgconfig:/opt/homebrew/opt/mpfr/lib/pkgconfig:/opt/homebrew/opt/libmpc/lib/pkgconfig:/opt/homebrew/opt/lz4/lib/pkgconfig:/opt/homebrew/opt/zstd/lib/pkgconfig:/opt/homebrew/opt/openblas/lib/pkgconfig:/opt/homebrew/opt/coinutils/lib/pkgconfig:/opt/homebrew/opt/osi/lib/pkgconfig:/opt/homebrew/opt/clp/lib/pkgconfig:/opt/homebrew/opt/cgl/lib/pkgconfig:/opt/homebrew/opt/cbc/lib/pkgconfig:/opt/homebrew/opt/mpdecimal/lib/pkgconfig:/opt/homebrew/opt/openssl@3/li

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GitHub Actions / build-bottles (ubuntu-latest)

`brew install --verbose --formula --build-bottle brewsci/bio/ntsynt` failed on Linux x86_64! 

      fout.write(asset.get_content())
                 ^^^^^^^^^^^^^^^^^^^
    File "/var/tmp/ntsynt--snakemake-20260711-2-qcdt1q/snakemake-8.19.0/snakemake/assets/__init__.py", line 29, in get_content
      raise AssetDownloadError(
  assets.AssetDownloadError: Checksum mismatch when downloading asset https://cdn.tailwindcss.com/3.0.23?plugins=forms@0.4.0,typography@0.5.2
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> No available output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /home/linuxbrew/.linuxbrew/Cellar/ntsynt/1.0.8/libexec/bin/python /home/linuxbrew/.linuxbrew/Cellar/python@3.12/3.12.13_4/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py get_requires_for_build_wheel /var/tmp/tmpxysbv862
  cwd: /var/tmp/ntsynt--snakemake-20260711-2-qcdt1q/snakemake-8.19.0
  Getting requirements to build wheel: finished with status 'error'
ERROR: Failed to build 'file:///var/tmp/ntsynt--snakemake-20260711-2-qcdt1q/snakemake-8.19.0' when getting requirements to build wheel

==> Formula
Tap: brewsci/bio
Path: /home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-bio/Formula/ntsynt.rb
==> Configuration
HOMEBREW_VERSION: 6.0.9-112-g34c40c1
ORIGIN: https://github.com/Homebrew/brew
HEAD: 34c40c18ffa2029b611b61c73273e32c003d0842
Last commit: 4 hours ago
Branch: main
Core tap: N/A
HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew
HOMEBREW_CACHE: /home/runner/.cache/Homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS: 3650
HOMEBREW_COLOR: set
HOMEBREW_CURL_PATH: /usr/bin/curl
HOMEBREW_DOWNLOAD_CONCURRENCY: 8
HOMEBREW_FAIL_LOG_LINES: 150
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_GIT_EMAIL: 1589480+BrewTestBot@users.noreply.github.com
HOMEBREW_GIT_NAME: BrewTestBot
HOMEBREW_GIT_PATH: /usr/bin/git
HOMEBREW_LOGS: /home/runner/work/homebrew-bio/homebrew-bio/logs
HOMEBREW_MAKE_JOBS: 4
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_EMOJI: set
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_REQUIRE_TAP_TRUST: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 4.0.5 => /home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/4.0.5_1/bin/ruby
CPU: quad-core 64-bit icelake
Clang: 22.1.8
Git: 2.54.0 => /usr/bin/git
Curl: 8.5.0 => /usr/bin/curl
Kernel: Linux 6.17.0-1018-azure x86_64 GNU/Linux
OS: Ubuntu 24.04.4 LTS (noble)
Host glibc: 2.39
Host libstdc++: 6.0.33
/usr/bin/gcc-13: 13.3.0
/usr/bin/ruby: 3.2.3
glibc: N/A
gcc@13: N/A
gcc: 16.1.0
xorg: N/A
==> ENV
CC: gcc
CXX: g++
OBJC: gcc
OBJCXX: g++
HOMEBREW_CC: gcc-13
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/shims/linux/super:/home/linuxbrew/.linuxbrew/opt/cython:/home/linuxbrew/.linuxbrew/opt/zlib:/home/linuxbrew/.linuxbrew
PKG_CONFIG_PATH: /home/linuxbrew/.linuxbrew/opt/xz/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/zlib-ng-compat/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/bzip2/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/gmp/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/isl/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/mpfr/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/libmpc/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/lz4/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/zstd/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/openblas/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/coinutils/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/osi/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/clp/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/cgl/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/cbc/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/mpdecimal/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/openssl@3/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/ncurses/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/readline/lib/pkgconfig:/home/linuxbrew/.linuxbrew/opt/sqlite/lib/pkgconfig:/home/linuxbr
venv = virtualenv_create(libexec, python3)
venv.pip_install resources
# pybedtools ships a legacy setup.py that imports pkg_resources, which was
# removed in setuptools >= 82. Install the other resources first (pinning
# setuptools 81), then build pybedtools with build isolation disabled so it
# uses the venv's pinned setuptools instead of fetching the latest.
venv.pip_install resources.reject { |r| r.name == "pybedtools" }
venv.pip_install resource("pybedtools"), build_isolation: false
# Remove the bundled CBC solver (Ref: homebrew-core/Formula/snakemake.rb)
rm_r(venv.site_packages/"pulp/solverdir/cbc")
# Use venv's python3 and snakemake
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