Date: Fri, 21 Jul 2023 22:24:21 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 29bea60c5980 - main - biology/btllib: New port: Bioinformatics Technology Lab common code library Message-ID: <202307212224.36LMOLpw088891@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=29bea60c598052bbf71415e494a179adbe143a8e commit 29bea60c598052bbf71415e494a179adbe143a8e Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2023-07-21 22:22:58 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2023-07-21 22:24:04 +0000 biology/btllib: New port: Bioinformatics Technology Lab common code library --- biology/Makefile | 1 + biology/btllib/Makefile | 30 ++++++++++++ biology/btllib/distinfo | 7 +++ biology/btllib/files/patch-meson.build | 54 ++++++++++++++++++++++ biology/btllib/files/patch-src_btllib_status.cpp | 18 ++++++++ .../files/patch-subprojects_cpptoml_CMakeLists.txt | 13 ++++++ biology/btllib/pkg-descr | 1 + biology/btllib/pkg-plist | 32 +++++++++++++ 8 files changed, 156 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 4f426e0a00ca..4f885c16edba 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -28,6 +28,7 @@ SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 + SUBDIR += btllib SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit diff --git a/biology/btllib/Makefile b/biology/btllib/Makefile new file mode 100644 index 000000000000..14d9616c5a00 --- /dev/null +++ b/biology/btllib/Makefile @@ -0,0 +1,30 @@ +PORTNAME= btllib +DISTVERSIONPREFIX= v +DISTVERSION= 1.6.2 +CATEGORIES= biology devel + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Bioinformatics Technology Lab common code library +WWW= https://github.com/bcgsc/btllib + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= bash:shells/bash \ + samtools:biology/samtools \ + cmake:devel/cmake-core +LIB_DEPENDS= libsdsl.so:devel/sdsl-lite +RUN_DEPENDS= samtools:biology/samtools + +USES= meson pkgconfig python:build shebangfix + +SHEBANG_FILES= scripts/* + +USE_GITHUB= yes +GH_ACCOUNT= bcgsc +GH_TUPLE= p-ranav:argparse:15d745f:argparse/subprojects/argparse \ + skystrife:cpptoml:fededad:cpptoml/subprojects/cpptoml + +BINARY_ALIAS= python3=${PYTHON_CMD} # python3-config=${PYTHON_CMD}-config # installs python binding into a wrong location, see https://github.com/bcgsc/btllib/issues/111 + +.include <bsd.port.mk> diff --git a/biology/btllib/distinfo b/biology/btllib/distinfo new file mode 100644 index 000000000000..4e0da820e3fc --- /dev/null +++ b/biology/btllib/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1689975725 +SHA256 (bcgsc-btllib-v1.6.2_GH0.tar.gz) = cba796cb83791e8524f5108459892a1131748cda55189c9acea21d4bdb80e7a0 +SIZE (bcgsc-btllib-v1.6.2_GH0.tar.gz) = 848942 +SHA256 (p-ranav-argparse-15d745f_GH0.tar.gz) = f033d4eb4a430b4ae4bf3c2a40e087709bf77462c1f9968ae07828437219a370 +SIZE (p-ranav-argparse-15d745f_GH0.tar.gz) = 105608 +SHA256 (skystrife-cpptoml-fededad_GH0.tar.gz) = dd2d129b67f537ae7d6f8d8d084c8c0d772d0f5b4b3118c1892e67ff536e335e +SIZE (skystrife-cpptoml-fededad_GH0.tar.gz) = 47398 diff --git a/biology/btllib/files/patch-meson.build b/biology/btllib/files/patch-meson.build new file mode 100644 index 000000000000..878516f5d78b --- /dev/null +++ b/biology/btllib/files/patch-meson.build @@ -0,0 +1,54 @@ +--- meson.build.orig 2023-07-06 15:52:18 UTC ++++ meson.build +@@ -1,7 +1,7 @@ + project('btllib', 'cpp', + version : '1.6.2', + license : 'GPL3', +- default_options : [ 'cpp_std=c++17', 'warning_level=3', 'werror=true', 'b_coverage=true' ], ++ default_options : [ 'cpp_std=c++17', 'warning_level=3', 'b_coverage=true' ], + meson_version : '>= 0.60.0') + + # Configuration +@@ -48,22 +48,28 @@ threads_dep = dependency('threads') + openmp_dep = dependency('openmp', required : false) + + cmake_options = cmake.subproject_options() +-cmake_options.set_override_option('werror', 'false') ++#cmake_options.set_override_option('werror', 'false') + cmake_options.set_install(false) + + cpptoml_subproject = cmake.subproject('cpptoml', options : cmake_options) + cpptomp_dep = cpptoml_subproject.dependency('cpptoml') + +-run_command(meson.project_source_root() + '/scripts/prepare-sdsl') ++#run_command(meson.project_source_root() + '/scripts/prepare-sdsl') + +-sdsl_subproject = cmake.subproject('sdsl-lite', options : cmake_options) +-sdsl_dep = sdsl_subproject.dependency('sdsl', include_type: 'system') ++#sdsl_subproject = cmake.subproject('sdsl-lite', options : cmake_options) + ++#sdsl_dep = sdsl_subproject.dependency('sdsl', include_type: 'system') ++ ++pkg = import('pkgconfig') ++sdsl_dep = dependency('sdsl-lite') ++#lib = library('foo', dependencies : [bar]) ++#pkg.generate(lib) ++ + deps = [ threads_dep, openmp_dep, cpptomp_dep, sdsl_dep ] + + # These are unfortunate hacks. Currently, neither cpptoml nor sdsl-lite install their headers (even when set_install(true) is called), and so we need to do it manually + meson.add_install_script('scripts/install-cpptoml') +-meson.add_install_script('scripts/install-sdsl-lite') ++#meson.add_install_script('scripts/install-sdsl-lite') + + argparse_subproject = cmake.subproject('argparse', options : cmake_options) + argparse_dep = argparse_subproject.dependency('argparse') +@@ -126,7 +132,7 @@ run_target('test-wrappers', command: join_paths(rootpa + btllib_include = [ include_directories('include'), include_directories('.') ] + btllib_sources = run_command('scripts/get-files', 'src').stdout().strip().split() + +-btllib_lib = static_library('btllib', ++btllib_lib = shared_library('btllib', + btllib_sources, + include_directories : btllib_include, + dependencies : deps, diff --git a/biology/btllib/files/patch-src_btllib_status.cpp b/biology/btllib/files/patch-src_btllib_status.cpp new file mode 100644 index 000000000000..930452d89fad --- /dev/null +++ b/biology/btllib/files/patch-src_btllib_status.cpp @@ -0,0 +1,18 @@ +--- src/btllib/status.cpp.orig 2023-07-21 18:23:40 UTC ++++ src/btllib/status.cpp +@@ -84,7 +84,7 @@ get_strerror() + char buf[buflen]; + // POSIX and GNU implementation of strerror_r differ, even in function signature + // and so we need to check which one is used +-#if __APPLE__ || \ ++#if __APPLE__ || __FreeBSD__ || \ + ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && !_GNU_SOURCE) + strerror_r(errno, buf, buflen); + return buf; +@@ -111,4 +111,4 @@ check_file_accessibility(const std::string& filepath) + btllib::check_error(ret != 0, get_strerror() + ": " + filepath); + } + +-} // namespace btllib +\ No newline at end of file ++} // namespace btllib diff --git a/biology/btllib/files/patch-subprojects_cpptoml_CMakeLists.txt b/biology/btllib/files/patch-subprojects_cpptoml_CMakeLists.txt new file mode 100644 index 000000000000..d660dd9b08b0 --- /dev/null +++ b/biology/btllib/files/patch-subprojects_cpptoml_CMakeLists.txt @@ -0,0 +1,13 @@ +--- subprojects/cpptoml/CMakeLists.txt.orig 2023-05-06 14:38:35 UTC ++++ subprojects/cpptoml/CMakeLists.txt +@@ -11,8 +11,8 @@ include(CMakePushCheckState) + + cmake_push_check_state() + +-option(ENABLE_LIBCXX "Use libc++ for the C++ standard library" ON) +-option(CPPTOML_BUILD_EXAMPLES "Build examples" ON) ++option(ENABLE_LIBCXX "Use libc++ for the C++ standard library" OFF) ++option(CPPTOML_BUILD_EXAMPLES "Build examples" OFF) + + set(CMAKE_EXPORT_COMPILE_COMMANDS 1) + diff --git a/biology/btllib/pkg-descr b/biology/btllib/pkg-descr new file mode 100644 index 000000000000..c802b1fe9d44 --- /dev/null +++ b/biology/btllib/pkg-descr @@ -0,0 +1 @@ +Bioinformatics Technology Lab's common code library in C++. diff --git a/biology/btllib/pkg-plist b/biology/btllib/pkg-plist new file mode 100644 index 000000000000..ccb8f845f30f --- /dev/null +++ b/biology/btllib/pkg-plist @@ -0,0 +1,32 @@ +bin/indexlr +bin/mi_bf_generate +bin/randseq +include/btllib/aahash.hpp +include/btllib/aahash_consts.hpp +include/btllib/bloom_filter.hpp +include/btllib/counting_bloom_filter-inl.hpp +include/btllib/counting_bloom_filter.hpp +include/btllib/cpptoml.h +include/btllib/cstring.hpp +include/btllib/data_stream.hpp +include/btllib/graph.hpp +include/btllib/indexlr.hpp +include/btllib/mi_bloom_filter-inl.hpp +include/btllib/mi_bloom_filter.hpp +include/btllib/nthash.hpp +include/btllib/nthash_consts.hpp +include/btllib/nthash_lowlevel.hpp +include/btllib/order_queue.hpp +include/btllib/process_pipeline.hpp +include/btllib/randseq.hpp +include/btllib/seq.hpp +include/btllib/seq_reader.hpp +include/btllib/seq_reader_fasta_module.hpp +include/btllib/seq_reader_fastq_module.hpp +include/btllib/seq_reader_multiline_fasta_module.hpp +include/btllib/seq_reader_multiline_fastq_module.hpp +include/btllib/seq_reader_sam_module.hpp +include/btllib/seq_writer.hpp +include/btllib/status.hpp +include/btllib/util.hpp +lib/libbtllib.so
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