nthash: add ver 2.3.0 + dependency

BioArchLinux/argparse/PKGBUILD

@@ -0,0 +1,26 @@
+# maintainer: JustKidding <jk@vin.ovh>
+pkgname=argparse
+pkgver=2.9
+pkgrel=1
+pkgdesc="Argument Parser for Modern C++"
+arch=(any)
+url="https://github.com/p-ranav/argparse"
+license=("MIT")
+makedepends=("cmake")
+source=("https://github.com/p-ranav/argparse/archive/v${pkgver}.tar.gz")
+sha512sums=("fa471e7d8c448510376e79927496f62775e6ed37e1dffefd607839e6005dfbc61125d0e18bfc1ff20f86cef7efd75339d7bb143dc6574d988f83c7c96896fa5f")
+
+build() {
+  cmake -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=/usr \
+        -B"${srcdir}/${pkgname}-${pkgver}" \
+        -H"${srcdir}/${pkgname}-${pkgver}"
+  cmake --build "${srcdir}/${pkgname}-${pkgver}"
+}
+
+package() {
+  make DESTDIR="${pkgdir}" -C "${srcdir}/${pkgname}-${pkgver}" install
+  install -Dm644 "${pkgname}-${pkgver}"/LICENSE "${pkgdir}"/usr/share/licenses/${pkgname}/LICENSE
+}
+
+# vim:set ts=2 sw=2 et:

BioArchLinux/argparse/lilac.yaml

@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: kbipinkumar
+    email: kbipinkumar@pm.me
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_pkgbuild_commit()
+update_on:
+- source: github
+  github: p-ranav/argparse
+  use_max_tag: true
+  prefix: 'v'

BioArchLinux/nthash/PKGBUILD

@@ -0,0 +1,42 @@
+# maintainer: bipin kumar <kbipinkumar@pm.me>
+pkgname=nthash-bcgsc
+_pkgname=ntHash
+pkgver=2.3.0
+pkgrel=1
+pkgdesc="Fast hash function for DNA/RNA sequences. https://doi.org/10.1093/bioinformatics/btac564"
+arch=('x86_64')
+url="https://bcgsc.github.io/ntHash/"
+license=('MIT')
+depends=('gcc-libs' 'glibc' 'zlib' 'zstd')
+makedepends=('cmake' 'btllib' 'argparse')
+source=("$pkgname-$pkgver.tar.gz::https://github.com/bcgsc/ntHash/archive/refs/tags/v${pkgver}.tar.gz"
+        "cmake.patch")
+sha256sums=('3115e140b50c9153c373e3a718d8e538e96724655caea7ed1bd2af1ef46f93da'
+            'dc38bef6af5497c79bec273539d511f49eba69e3dec72a299def3d5d9d530f7d')
+
+prepare(){
+    cd "$_pkgname-$pkgver"
+    patch -p1 < "${srcdir}"/cmake.patch
+}
+build() {
+    cmake -B build -S "$_pkgname-$pkgver" \
+        -DCMAKE_BUILD_TYPE='None' \
+        -DCMAKE_INSTALL_PREFIX='/usr' \
+        -Wno-dev
+    cmake --build build
+}
+
+check() {
+    ctest --test-dir build --output-on-failure
+}
+
+package() {
+    install -Dm644 "$_pkgname-$pkgver"/LICENSE "${pkgdir}"/usr/share/licenses/${pkgname}/LICENSE
+    install -Dm755 ${srcdir}/build/nthash "${pkgdir}"/usr/bin/nthash
+    install -Dm644 ${srcdir}/build/libnthash.a "${pkgdir}"/usr/lib/libnthash.a
+
+    for file in "${_pkgname}-${pkgver}"/include/nthash/*.hpp ; do
+        install -Dm644 "${file}" "${pkgdir}"/usr/include/${pkgname}/"${file}"
+    done
+}
+  

BioArchLinux/nthash/cmake.patch

@@ -0,0 +1,34 @@
+--- ntHash-2.3.0.orig/CMakeLists.txt	2022-09-02 01:19:04.000000000 +0530
++++ ntHash-2.3.0.new/CMakeLists.txt	2023-10-23 15:25:37.360088916 +0530
+@@ -12,25 +12,20 @@
+ set(CMAKE_CXX_FLAGS_RELEASE "-O3")
+ 
+ include_directories(include)
+-include_directories(vendor/btllib/include)
+-include_directories(vendor/argparse/include)
++include_directories(/usr/include)
++include_directories(/usr/include)
+ 
+ file(GLOB SRC_FILES ${PROJECT_SOURCE_DIR}/src/nthash/*.cpp)
+ 
+-add_custom_command(
+-        OUTPUT ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a
+-        COMMAND ${PROJECT_SOURCE_DIR}/vendor/btllib/compile --prefix ${PROJECT_BINARY_DIR}/btllib
+-)
+-
+ add_library(nthash_lib STATIC ${SRC_FILES})
+ set_target_properties(nthash_lib PROPERTIES OUTPUT_NAME "nthash")
+ 
+-add_executable(nthash main.cpp ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a)
+-target_link_libraries(nthash ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a)
++add_executable(nthash main.cpp /usr/lib/libbtllib.a)
++target_link_libraries(nthash /usr/lib/libbtllib.a)
+ target_link_libraries(nthash ${PROJECT_BINARY_DIR}/libnthash.a)
+ 
+-add_executable(nthash_tests ${PROJECT_SOURCE_DIR}/tests/tests.cpp ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a)
+-target_link_libraries(nthash_tests ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a)
++add_executable(nthash_tests ${PROJECT_SOURCE_DIR}/tests/tests.cpp /usr/lib/libbtllib.a)
++target_link_libraries(nthash_tests /usr/lib/libbtllib.a)
+ target_link_libraries(nthash_tests ${PROJECT_BINARY_DIR}/libnthash.a)
+ enable_testing()
+ add_test(NAME nthash_tests COMMAND $<TARGET_FILE:nthash_tests>)

BioArchLinux/nthash/lilac.yaml

@@ -0,0 +1,18 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: kbipinkumar
+    email: kbipinkumar@pm.me
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_pkgbuild_commit()
+  update_aur_repo()
+repo_depends:
+  - btllib
+  - argparse
+update_on:
+- source: github
+  github: bcgsc/ntHash
+  use_max_tag: true
+  prefix: 'v'