mmseqs: version 15-6f452

BioArchLinux/mmseqs2/PKGBUILD

@@ -0,0 +1,77 @@
+# maintainer: bipin <kbipinkumar@pm.me>
+pkgbase=mmseqs2
+pkgname=('mmseqs2-sse4' 'mmseqs2-avx2')
+_pkgbase=${pkgbase//mm/MM}
+pkgver=15.6f452
+_pkgver=15-6f452
+pkgrel=1
+pkgdesc="ultra fast and sensitive search and clustering suite. https://doi.org/10.1038/nbt.3988"
+arch=('x86_64')
+url="https://github.com/soedinglab/mmseqs2"
+license=('GPL3')
+makedepends=('cmake' 'zlib' 'openmp' 'vim')
+source=("$_pkgbase-$_pkgver.tar.gz::https://github.com/soedinglab/MMseqs2/archive/refs/tags/${_pkgver}.tar.gz")
+sha256sums=('7115ac5a7e2a49229466806aaa760d00204bb08c870e3c231b00e525c77531dc')
+
+build() {
+  cd $_pkgbase-$_pkgver
+  # 'mmseqs2-sse4'
+  cmake -B build1 \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DCMAKE_BUILD_TYPE=None  \
+    -DHAVE_SSE4_1=1 \
+    -DNATIVE_ARCH=0 \
+    -DCMAKE_C_FLAGS="${CFLAGS} ${CPPFLAGS}" \
+    -DCMAKE_CXX_FLAGS="${CXXFLAGS} ${CPPFLAGS}" \
+    -DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \
+    -DCMAKE_SHARED_LINKER_FLAGS="${LDFLAGS}" \
+    -Wno-dev \
+    -DVERSION_OVERRIDE="${_pkgver}"-BioArchLinux_sse4
+
+  # 'mmseqs2-AVX2'
+  cmake -B build2 \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DCMAKE_BUILD_TYPE=None \
+    -DNATIVE_ARCH=0 \
+    -DHAVE_AVX2=1 \
+    -DCMAKE_C_FLAGS="${CFLAGS} ${CPPFLAGS}" \
+    -DCMAKE_CXX_FLAGS="${CXXFLAGS} ${CPPFLAGS}" \
+    -DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \
+    -DCMAKE_SHARED_LINKER_FLAGS="${LDFLAGS}" \
+    -Wno-dev \
+    -DVERSION_OVERRIDE="${_pkgver}"-BioArchLinux_avx2
+
+    # Build 'mmseqs2-sse4'
+   MAKEFLAGS=-j1 cmake --build build1
+   # Build 'mmseqs2-AVX2'
+   MAKEFLAGS=-j1 cmake --build build2
+
+}
+
+package_mmseqs2-sse4() {
+  depends=('gcc-libs' 'glibc' 'zlib' 'zstd' 'openmp' 'bzip2' 'bash')
+  provides=('mmseqs2')
+  conflicts=('mmseqs2-avx2')
+  pkgdesc="ultra fast and sensitive search and clustering suite optimised for SSE4 instructions. https://doi.org/10.1038/nbt.3988"
+
+  cd $_pkgbase-$_pkgver
+  DESTDIR="$pkgdir" cmake --install build1
+  cd util
+  install -Dm755 bash-completion.sh "${pkgdir}"/etc/profile.d/mmseqs2-completion.sh
+  install -Dm755 format_substitution_matrix.R ${pkgdir}/usr/share/${pkgbase}/format_substitution_matrix.R
+  rm -rf "${pkgdir}"/usr/util
+}
+
+package_mmseqs2-avx2() {
+  depends=('gcc-libs' 'glibc' 'zlib' 'zstd' 'openmp' 'bzip2' 'bash')
+  provides=('mmseqs2')
+  conflicts=('mmseqs2-sse4')
+  pkgdesc="ultra fast and sensitive search and clustering suite optimised for AVX2 instructions. https://doi.org/10.1038/nbt.3988"
+
+  cd $_pkgbase-$_pkgver
+  DESTDIR="$pkgdir" cmake --install build2
+  cd util
+  install -Dm755 bash-completion.sh "${pkgdir}"/etc/profile.d/mmseqs2-completion.sh
+  install -Dm755 format_substitution_matrix.R ${pkgdir}/usr/share/${pkgbase}/format_substitution_matrix.R
+  rm -rf "${pkgdir}"/usr/util
+}

BioArchLinux/mmseqs2/lilac.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+def pre_build():
+    for line in edit_file('PKGBUILD'):
+        if line.startswith('_pkgver='):
+            line = f'_pkgver={_G.newver}'
+        print(line)
+    update_pkgver_and_pkgrel(_G.newver.replace('-', '.'))
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/mmseqs2/lilac.yaml

@@ -0,0 +1,14 @@
+maintainers:
+  - github: kbipinkumar
+    email: kbipinkumar@pm.me
+build_prefix: extra-x86_64
+update_on:
+  - source: manual
+    manual: 15-6f452
+time_limit_hours: 2
+
+update_on:
+  - source: github
+    github: soedinglab/MMseqs2
+    use_latest_release: true
+    prefix: 'v'