biology/seqan3 3.4.2 FreeBSD
C++ header-only library for biological sequence analysis
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- BSD3CLAUSE
- Categories
- biology, devel, math
- Package size
- 642.9 KiB, 5209.9 KiB installed
Description
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
Install
Binary package:
pkg install seqan3From the ports tree:
cd /usr/ports/biology/seqan3/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= seqan3>0:biology/seqan3Packages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 3.4.2 | 3.4.2 | - | 3.3.0 | 3.4.2 |
| FreeBSD:14:quarterly | 3.4.2 | 3.4.2 | n/a | 3.3.0 | 3.4.2 |
| FreeBSD:15:latest | 3.4.2 | 3.4.2 | n/a | 3.3.0 | 3.4.0 |
| FreeBSD:15:quarterly | 3.4.2 | 3.4.2 | n/a | n/a | n/a |
| FreeBSD:16:latest | 3.4.2 | 3.4.2 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 2
cereal>0: devel/cerealrange-v3>0: devel/range-v3
Runtime 3
cereal>0: devel/cerealrange-v3>0: devel/range-v3coin-or-lemon>0: math/lemon
The full lists below include those, and their dependencies in turn.
Build dependencies 21
Run dependencies 28
- archivers/liblz4
- archivers/zstd
- devel/binutils
- devel/boost-libs
- devel/cereal
- devel/icu
- devel/range-v3
- lang/gcc14
- math/asl
- math/blas
- math/cbc
- math/cgl
- math/clp
- math/coin-or-data-netlib
- math/coin-or-data-sample
- math/coin-or-metis
- math/coin-or-mumps
- math/coinutils
- math/glpk
- math/gmp
- math/lapack
- math/lemon
- math/mpc
- math/mpfr
- math/nauty
- math/openblas
- math/osi
- print/indexinfo
No port depends on this one.
Configuration
No options to configure.
- USES
- cmake compiler:c++23-lang localbase
- Service scripts
- none
Files
pkg-plist 459
- 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/cigar_conversion/alignment_from_cigar.hpp
- include/seqan3/alignment/cigar_conversion/all.hpp
- include/seqan3/alignment/cigar_conversion/cigar_from_alignment.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/all.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/all.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_optimum.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/debug_matrix.hpp
- include/seqan3/alignment/matrix/detail/edit_distance_score_matrix_full.hpp
- include/seqan3/alignment/matrix/detail/edit_distance_trace_matrix_full.hpp
- include/seqan3/alignment/matrix/detail/matrix_concept.hpp
- include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp
- include/seqan3/alignment/matrix/detail/row_wise_matrix.hpp
- include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp
- include/seqan3/alignment/matrix/detail/trace_directions.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/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/hamming_scoring_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
The first 100 are listed.
distinfo 3
| File | Size | SHA256 |
|---|---|---|
| seqan3-3.4.2/CPM.cmake | 44969 | f3a6dcc6a04ce9e7f51a127307fa4f699fb2bade357a8eb4c5b45df76e1dc6a5 |
| seqan3-3.4.2/seqan-seqan3-3.4.2_GH0.tar.gz | 1.752849e+06 | bb7467f8e296279a89fa75909129e128d67195187fe066ed096e9fb6250e37e5 |
| seqan3-3.4.2/xxsds-sdsl-lite-d54d389_GH0.tar.gz | 1.183835e+06 | eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1 |
Master sites 1
- https://github.com/cpm-cmake/CPM.cmake/releases/download/v0.42.1/:cpm
Commit history 0
No commits in the history this site was built from.