Date: Wed, 12 May 2021 01:21:41 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: 37be6965367e - main - New port: biology/seqan3: C++ header-only library for biological sequence analysis Message-ID: <202105120121.14C1LfAg079186@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=37be6965367eec49bc848623a2ad782d8f74471a commit 37be6965367eec49bc848623a2ad782d8f74471a Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2021-05-12 01:20:55 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2021-05-12 01:21:38 +0000 New port: biology/seqan3: C++ header-only library for biological sequence analysis --- biology/Makefile | 1 + biology/seqan3/Makefile | 28 ++ biology/seqan3/distinfo | 5 + biology/seqan3/pkg-descr | 9 + biology/seqan3/pkg-plist | 673 +++++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 716 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 358a2c77403e..e5bec235ca01 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -164,6 +164,7 @@ SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 + SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile new file mode 100644 index 000000000000..09dc6766ff68 --- /dev/null +++ b/biology/seqan3/Makefile @@ -0,0 +1,28 @@ +PORTNAME= seqan3 +DISTVERSION= 3.0.2-1195 +DISTVERSIONSUFFIX= -gee0dbcad +CATEGORIES= biology devel math + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ header-only library for biological sequence analysis + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.md + +HPP_DEPENDS= cereal>0:devel/cereal \ + coin-or-lemon>0:math/lemon \ + range-v3>0:devel/range-v3 +BUILD_DEPENDS= ${HPP_DEPENDS} + +USES= cmake localbase + +USE_GITHUB= yes +GH_ACCOUNT= seqan +GH_TUPLE= xxsds:sdsl-lite:9a0d567:sdsl_lite/submodules/sdsl-lite + +NO_ARCH= yes + +post-install: + @${RM} -r ${STAGEDIR}${DOCSDIR} + +.include <bsd.port.mk> diff --git a/biology/seqan3/distinfo b/biology/seqan3/distinfo new file mode 100644 index 000000000000..408948c836d6 --- /dev/null +++ b/biology/seqan3/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1620779602 +SHA256 (seqan-seqan3-3.0.2-1195-gee0dbcad_GH0.tar.gz) = 6a838f97be0c850e46141fa9afa081f76ce9196e64e395ce8928da7e7fb73cd9 +SIZE (seqan-seqan3-3.0.2-1195-gee0dbcad_GH0.tar.gz) = 1456878 +SHA256 (xxsds-sdsl-lite-9a0d567_GH0.tar.gz) = 1727ec6897535a493b99ff36a6d19d8205964be2b2a027ba547fc77ab7dbd74e +SIZE (xxsds-sdsl-lite-9a0d567_GH0.tar.gz) = 1156974 diff --git a/biology/seqan3/pkg-descr b/biology/seqan3/pkg-descr new file mode 100644 index 000000000000..8cb4595b3673 --- /dev/null +++ b/biology/seqan3/pkg-descr @@ -0,0 +1,9 @@ +SeqAn3 is the new version of the popular SeqAn template library for the analysis +of biological sequences. It enables the rapid development of high-performance +solutions by providing generic algorithms and data structures for: +* sequence representation and transformation +* full-text indexing and efficient search +* sequence alignment +* input/output of common file formats + +WWW: https://github.com/seqan/seqan3 diff --git a/biology/seqan3/pkg-plist b/biology/seqan3/pkg-plist new file mode 100644 index 000000000000..675c0f36cead --- /dev/null +++ b/biology/seqan3/pkg-plist @@ -0,0 +1,673 @@ +include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp +include/seqan3/alignment/aligned_sequence/all.hpp +include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp +include/seqan3/alignment/all.hpp +include/seqan3/alignment/band/all.hpp +include/seqan3/alignment/band/static_band.hpp +include/seqan3/alignment/configuration/align_config_band.hpp +include/seqan3/alignment/configuration/align_config_debug.hpp +include/seqan3/alignment/configuration/align_config_edit.hpp +include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp +include/seqan3/alignment/configuration/align_config_method.hpp +include/seqan3/alignment/configuration/align_config_min_score.hpp +include/seqan3/alignment/configuration/align_config_on_result.hpp +include/seqan3/alignment/configuration/align_config_output.hpp +include/seqan3/alignment/configuration/align_config_parallel.hpp +include/seqan3/alignment/configuration/align_config_result_type.hpp +include/seqan3/alignment/configuration/align_config_score_type.hpp +include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp +include/seqan3/alignment/configuration/align_config_vectorised.hpp +include/seqan3/alignment/configuration/all.hpp +include/seqan3/alignment/configuration/detail.hpp +include/seqan3/alignment/decorator/gap_decorator.hpp +include/seqan3/alignment/detail/pairwise_alignment_concept.hpp +include/seqan3/alignment/exception.hpp +include/seqan3/alignment/matrix/alignment_coordinate.hpp +include/seqan3/alignment/matrix/alignment_optimum.hpp +include/seqan3/alignment/matrix/all.hpp +include/seqan3/alignment/matrix/debug_matrix.hpp +include/seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp +include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp +include/seqan3/alignment/matrix/detail/aligned_sequence_builder.hpp +include/seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp +include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp +include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_banded.hpp +include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp +include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp +include/seqan3/alignment/matrix/detail/alignment_trace_matrix_base.hpp +include/seqan3/alignment/matrix/detail/alignment_trace_matrix_full.hpp +include/seqan3/alignment/matrix/detail/alignment_trace_matrix_full_banded.hpp +include/seqan3/alignment/matrix/detail/alignment_trace_matrix_proxy.hpp +include/seqan3/alignment/matrix/detail/all.hpp +include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp +include/seqan3/alignment/matrix/detail/coordinate_matrix.hpp +include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp +include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp +include/seqan3/alignment/matrix/detail/trace_iterator.hpp +include/seqan3/alignment/matrix/detail/trace_iterator_banded.hpp +include/seqan3/alignment/matrix/detail/trace_iterator_base.hpp +include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp +include/seqan3/alignment/matrix/detail/two_dimensional_matrix.hpp +include/seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_base.hpp +include/seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_concept.hpp +include/seqan3/alignment/matrix/edit_distance_score_matrix_full.hpp +include/seqan3/alignment/matrix/edit_distance_trace_matrix_full.hpp +include/seqan3/alignment/matrix/matrix_concept.hpp +include/seqan3/alignment/matrix/row_wise_matrix.hpp +include/seqan3/alignment/matrix/trace_directions.hpp +include/seqan3/alignment/pairwise/align_pairwise.hpp +include/seqan3/alignment/pairwise/align_result_selector.hpp +include/seqan3/alignment/pairwise/alignment_algorithm.hpp +include/seqan3/alignment/pairwise/alignment_configurator.hpp +include/seqan3/alignment/pairwise/alignment_result.hpp +include/seqan3/alignment/pairwise/all.hpp +include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp +include/seqan3/alignment/pairwise/detail/concept.hpp +include/seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm.hpp +include/seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm_banded.hpp +include/seqan3/alignment/pairwise/detail/policy_affine_gap_recursion.hpp +include/seqan3/alignment/pairwise/detail/policy_affine_gap_recursion_banded.hpp +include/seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion.hpp +include/seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion_banded.hpp +include/seqan3/alignment/pairwise/detail/policy_alignment_matrix.hpp +include/seqan3/alignment/pairwise/detail/policy_alignment_result_builder.hpp +include/seqan3/alignment/pairwise/detail/policy_optimum_tracker.hpp +include/seqan3/alignment/pairwise/detail/policy_optimum_tracker_simd.hpp +include/seqan3/alignment/pairwise/detail/policy_scoring_scheme.hpp +include/seqan3/alignment/pairwise/detail/type_traits.hpp +include/seqan3/alignment/pairwise/edit_distance_algorithm.hpp +include/seqan3/alignment/pairwise/edit_distance_fwd.hpp +include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp +include/seqan3/alignment/pairwise/policy/affine_gap_init_policy.hpp +include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp +include/seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp +include/seqan3/alignment/pairwise/policy/all.hpp +include/seqan3/alignment/pairwise/policy/find_optimum_policy.hpp +include/seqan3/alignment/pairwise/policy/scoring_scheme_policy.hpp +include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp +include/seqan3/alignment/pairwise/policy/simd_find_optimum_policy.hpp +include/seqan3/alignment/scoring/all.hpp +include/seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp +include/seqan3/alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp +include/seqan3/alignment/scoring/detail/simd_matrix_scoring_scheme.hpp +include/seqan3/alignment/scoring/gap_scheme.hpp +include/seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp +include/seqan3/alignment/scoring/scoring_scheme_base.hpp +include/seqan3/alignment/scoring/scoring_scheme_concept.hpp +include/seqan3/alphabet/adaptation/all.hpp +include/seqan3/alphabet/adaptation/char.hpp +include/seqan3/alphabet/adaptation/uint.hpp +include/seqan3/alphabet/all.hpp +include/seqan3/alphabet/alphabet_base.hpp +include/seqan3/alphabet/aminoacid/aa10li.hpp +include/seqan3/alphabet/aminoacid/aa10murphy.hpp +include/seqan3/alphabet/aminoacid/aa20.hpp +include/seqan3/alphabet/aminoacid/aa27.hpp +include/seqan3/alphabet/aminoacid/all.hpp +include/seqan3/alphabet/aminoacid/aminoacid_base.hpp +include/seqan3/alphabet/aminoacid/concept.hpp +include/seqan3/alphabet/aminoacid/translation.hpp +include/seqan3/alphabet/aminoacid/translation_details.hpp +include/seqan3/alphabet/aminoacid/translation_genetic_code.hpp +include/seqan3/alphabet/cigar/all.hpp +include/seqan3/alphabet/cigar/cigar.hpp +include/seqan3/alphabet/cigar/cigar_op.hpp +include/seqan3/alphabet/cigar/exposition_only/cigar_operation.hpp +include/seqan3/alphabet/composite/all.hpp +include/seqan3/alphabet/composite/alphabet_tuple_base.hpp +include/seqan3/alphabet/composite/alphabet_variant.hpp +include/seqan3/alphabet/composite/detail.hpp +include/seqan3/alphabet/composite/semialphabet_any.hpp +include/seqan3/alphabet/concept.hpp +include/seqan3/alphabet/container/bitpacked_sequence.hpp +include/seqan3/alphabet/container/concatenated_sequences.hpp +include/seqan3/alphabet/detail/alphabet_proxy.hpp +include/seqan3/alphabet/detail/convert.hpp +include/seqan3/alphabet/exception.hpp +include/seqan3/alphabet/gap/all.hpp +include/seqan3/alphabet/gap/gap.hpp +include/seqan3/alphabet/gap/gapped.hpp +include/seqan3/alphabet/hash.hpp +include/seqan3/alphabet/mask/all.hpp +include/seqan3/alphabet/mask/mask.hpp +include/seqan3/alphabet/mask/masked.hpp +include/seqan3/alphabet/nucleotide/all.hpp +include/seqan3/alphabet/nucleotide/concept.hpp +include/seqan3/alphabet/nucleotide/dna15.hpp +include/seqan3/alphabet/nucleotide/dna16sam.hpp +include/seqan3/alphabet/nucleotide/dna3bs.hpp +include/seqan3/alphabet/nucleotide/dna4.hpp +include/seqan3/alphabet/nucleotide/dna5.hpp +include/seqan3/alphabet/nucleotide/nucleotide_base.hpp +include/seqan3/alphabet/nucleotide/rna15.hpp +include/seqan3/alphabet/nucleotide/rna4.hpp +include/seqan3/alphabet/nucleotide/rna5.hpp +include/seqan3/alphabet/nucleotide/sam_dna16.hpp +include/seqan3/alphabet/quality/aliases.hpp +include/seqan3/alphabet/quality/all.hpp +include/seqan3/alphabet/quality/concept.hpp +include/seqan3/alphabet/quality/phred42.hpp +include/seqan3/alphabet/quality/phred63.hpp +include/seqan3/alphabet/quality/phred68legacy.hpp +include/seqan3/alphabet/quality/phred68solexa.hpp +include/seqan3/alphabet/quality/phred94.hpp +include/seqan3/alphabet/quality/phred_base.hpp +include/seqan3/alphabet/quality/qualified.hpp +include/seqan3/alphabet/quality/quality_base.hpp +include/seqan3/alphabet/range/hash.hpp +include/seqan3/alphabet/range/sequence.hpp +include/seqan3/alphabet/structure/all.hpp +include/seqan3/alphabet/structure/concept.hpp +include/seqan3/alphabet/structure/dot_bracket3.hpp +include/seqan3/alphabet/structure/dssp9.hpp +include/seqan3/alphabet/structure/structured_aa.hpp +include/seqan3/alphabet/structure/structured_rna.hpp +include/seqan3/alphabet/structure/wuss.hpp +include/seqan3/alphabet/views/all.hpp +include/seqan3/alphabet/views/char_to.hpp +include/seqan3/alphabet/views/complement.hpp +include/seqan3/alphabet/views/rank_to.hpp +include/seqan3/alphabet/views/to_char.hpp +include/seqan3/alphabet/views/to_rank.hpp +include/seqan3/alphabet/views/translate.hpp +include/seqan3/alphabet/views/translate_join.hpp +include/seqan3/alphabet/views/trim_quality.hpp +include/seqan3/argument_parser/all.hpp +include/seqan3/argument_parser/argument_parser.hpp +include/seqan3/argument_parser/auxiliary.hpp +include/seqan3/argument_parser/detail/format_base.hpp +include/seqan3/argument_parser/detail/format_help.hpp +include/seqan3/argument_parser/detail/format_html.hpp +include/seqan3/argument_parser/detail/format_man.hpp +include/seqan3/argument_parser/detail/format_parse.hpp +include/seqan3/argument_parser/detail/terminal.hpp +include/seqan3/argument_parser/detail/version_check.hpp +include/seqan3/argument_parser/exceptions.hpp +include/seqan3/argument_parser/validators.hpp +include/seqan3/contrib/charconv/LICENSE.TXT +include/seqan3/contrib/charconv/charconv +include/seqan3/contrib/charconv/charconv.cpp +include/seqan3/contrib/charconv/charconv_pre.hpp +include/seqan3/contrib/parallel/buffer_queue.hpp +include/seqan3/contrib/parallel/serialised_resource_pool.hpp +include/seqan3/contrib/parallel/suspendable_queue.hpp +include/seqan3/contrib/span/span +include/seqan3/contrib/stream/bgzf_istream.hpp +include/seqan3/contrib/stream/bgzf_ostream.hpp +include/seqan3/contrib/stream/bgzf_stream_util.hpp +include/seqan3/contrib/stream/bz2_istream.hpp +include/seqan3/contrib/stream/bz2_ostream.hpp +include/seqan3/contrib/stream/gz_istream.hpp +include/seqan3/contrib/stream/gz_ostream.hpp +include/seqan3/core/add_enum_bitwise_operators.hpp +include/seqan3/core/algorithm/algorithm_result_generator_range.hpp 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+include/seqan3/core/type_traits/transformation_trait_or.hpp +include/seqan3/io/alignment_file/all.hpp +include/seqan3/io/alignment_file/detail.hpp +include/seqan3/io/alignment_file/format_bam.hpp +include/seqan3/io/alignment_file/format_sam.hpp +include/seqan3/io/alignment_file/format_sam_base.hpp +include/seqan3/io/alignment_file/header.hpp +include/seqan3/io/alignment_file/input.hpp +include/seqan3/io/alignment_file/input_format_concept.hpp +include/seqan3/io/alignment_file/input_options.hpp +include/seqan3/io/alignment_file/misc.hpp +include/seqan3/io/alignment_file/output.hpp +include/seqan3/io/alignment_file/output_format_concept.hpp +include/seqan3/io/alignment_file/output_options.hpp +include/seqan3/io/alignment_file/sam_tag_dictionary.hpp +include/seqan3/io/all.hpp +include/seqan3/io/detail/ignore_output_iterator.hpp +include/seqan3/io/detail/in_file_iterator.hpp +include/seqan3/io/detail/istreambuf_view.hpp +include/seqan3/io/detail/magic_header.hpp 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