diff options
| author | yuri <yuri@FreeBSD.org> | 2018-03-10 14:21:37 +0800 |
|---|---|---|
| committer | yuri <yuri@FreeBSD.org> | 2018-03-10 14:21:37 +0800 |
| commit | a2484added305288909c97bf1c49134d0153f93f (patch) | |
| tree | fea76f19685ea567c95e91bf74ab4536e153b256 /biology/seqan | |
| parent | a09b8da077287e9bce1f0bb656a43590e4062fad (diff) | |
| download | freebsd-ports-gnome-a2484added305288909c97bf1c49134d0153f93f.tar.gz freebsd-ports-gnome-a2484added305288909c97bf1c49134d0153f93f.tar.zst freebsd-ports-gnome-a2484added305288909c97bf1c49134d0153f93f.zip | |
biology/seqan-apps, biology/seqan: Update to 2.4.0
Port changes for biology/seqan-apps:
* Changed to DISTVERSION
* Updated COMMENT
* Added USES=compiler:openmp
* Removed BROKEN_xx (upstream now claims support for these architectures)
* Removed USE_GCC
* Added SSE4/AVX2/NATIVE SIMD options
Port changes for biology/seqan:
* Changed to DISTVERSION
* Added NO_ARCH
* Added PORTDOCS=*
* Updated do-install
PR: 225682
Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
Approved by: tcberner (mentor, implicit)
Diffstat (limited to 'biology/seqan')
| -rw-r--r-- | biology/seqan/Makefile | 17 | ||||
| -rw-r--r-- | biology/seqan/distinfo | 6 | ||||
| -rw-r--r-- | biology/seqan/pkg-descr | 6 | ||||
| -rw-r--r-- | biology/seqan/pkg-plist | 1298 |
4 files changed, 75 insertions, 1252 deletions
diff --git a/biology/seqan/Makefile b/biology/seqan/Makefile index b5974688a8e6..71f4951ffb23 100644 --- a/biology/seqan/Makefile +++ b/biology/seqan/Makefile @@ -2,30 +2,35 @@ # $FreeBSD$ PORTNAME= seqan -PORTVERSION= 2.2.0 +DISTVERSION= 2.4.0 CATEGORIES= biology MASTER_SITES= http://packages.seqan.de/seqan-library/ DISTNAME= ${PORTNAME}-library-${PORTVERSION} MAINTAINER= h2+fbsdports@fsfe.org -COMMENT= C++ Sequence Analysis Template Library +COMMENT= C++ sequence analysis template library LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/share/doc/seqan/LICENSE USES= tar:xz NO_BUILD= yes +NO_ARCH= yes CONFLICTS= seqan1-[0-9]* OPTIONS_DEFINE= DOCS -DOCS_DESC= Install official API documentation (html) + +PORTDOCS= * + +post-patch: # delete empty doc dirs + @cd ${WRKSRC}/share/doc/seqan/html && ${RMDIR} docs/seqan docs lists do-install: cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include - ${MKDIR} ${STAGEDIR}/${PREFIX}/share/cmake/Modules - ${INSTALL_DATA} ${WRKSRC}/share/cmake/Modules/FindSeqAn.cmake ${STAGEDIR}/${PREFIX}/share/cmake/Modules/ - ${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig + @${MKDIR} ${STAGEDIR}/${PREFIX}/lib/cmake/seqan + ${INSTALL_DATA} ${WRKSRC}/share/cmake/seqan/seqan-config.cmake ${STAGEDIR}/${PREFIX}/lib/cmake/seqan/ + @${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig ${INSTALL_DATA} ${WRKSRC}/share/pkgconfig/seqan-2.pc ${STAGEDIR}/${PREFIX}/libdata/pkgconfig/ do-install-DOCS-on: diff --git a/biology/seqan/distinfo b/biology/seqan/distinfo index 18175fb6bde5..62db7cc16085 100644 --- a/biology/seqan/distinfo +++ b/biology/seqan/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1473846790 -SHA256 (seqan-library-2.2.0.tar.xz) = b5c036a3d2fc2fe5f2d57dcd4d7c523a6df146ab7b44bc789f42004b058d72fd -SIZE (seqan-library-2.2.0.tar.xz) = 5223004 +TIMESTAMP = 1517832492 +SHA256 (seqan-library-2.4.0.tar.xz) = dd97b1514ab83acb7d7be911b157979e188e8ca72cc61c430c1e0fd03bcd41a5 +SIZE (seqan-library-2.4.0.tar.xz) = 4868868 diff --git a/biology/seqan/pkg-descr b/biology/seqan/pkg-descr index 705046885848..890a5a4e160d 100644 --- a/biology/seqan/pkg-descr +++ b/biology/seqan/pkg-descr @@ -3,7 +3,7 @@ and data structures for the analysis of sequences with the focus on biological data. The library is licensed under the 3-clause BSD license except the applications which are GPL. -This port now only contains the header library and API -documentation. The apps are separate. +This port only contains the header library and API documentation. +The apps are installed by biology/seqan-apps. -WWW: http://www.seqan.de/ +WWW: https://www.seqan.de/ diff --git a/biology/seqan/pkg-plist b/biology/seqan/pkg-plist index 5d6f426890ff..0f486c3fd5a1 100644 --- a/biology/seqan/pkg-plist +++ b/biology/seqan/pkg-plist @@ -6,6 +6,7 @@ include/seqan/align/align_interface_wrapper.h include/seqan/align/align_iterator_base.h include/seqan/align/align_metafunctions.h include/seqan/align/align_traceback.h +include/seqan/align/aligned_sequence_concept.h include/seqan/align/alignment_algorithm_tags.h include/seqan/align/alignment_operations.h include/seqan/align/dp_algorithm_impl.h @@ -62,6 +63,26 @@ include/seqan/align_extend.h include/seqan/align_extend/align_extend.h include/seqan/align_extend/align_extend_base.h include/seqan/align_extend/dp_scout_xdrop.h +include/seqan/align_parallel.h +include/seqan/align_parallel/async_wave_execution_interface.h +include/seqan/align_parallel/dp_kernel_adaptor.h +include/seqan/align_parallel/dp_parallel_execution_policies.h +include/seqan/align_parallel/dp_parallel_scout.h +include/seqan/align_parallel/dp_parallel_scout_simd.h +include/seqan/align_parallel/dp_settings.h +include/seqan/align_parallel/dp_traits.h +include/seqan/align_parallel/parallel_align_interface.h +include/seqan/align_parallel/wavefront_alignment_executor.h +include/seqan/align_parallel/wavefront_alignment_result.h +include/seqan/align_parallel/wavefront_alignment_scheduler.h +include/seqan/align_parallel/wavefront_alignment_task.h +include/seqan/align_parallel/wavefront_alignment_thread_local_storage.h +include/seqan/align_parallel/wavefront_task.h +include/seqan/align_parallel/wavefront_task_event.h +include/seqan/align_parallel/wavefront_task_executor.h +include/seqan/align_parallel/wavefront_task_queue.h +include/seqan/align_parallel/wavefront_task_scheduler.h +include/seqan/align_parallel/wavefront_task_util.h include/seqan/align_profile.h include/seqan/align_profile/add_to_profile.h include/seqan/align_profile/score_profile_seq.h @@ -84,6 +105,7 @@ include/seqan/arg_parse/arg_parse_exceptions.h include/seqan/arg_parse/arg_parse_option.h include/seqan/arg_parse/arg_parse_parse.h include/seqan/arg_parse/arg_parse_type_support.h +include/seqan/arg_parse/arg_parse_version_check.h include/seqan/arg_parse/argument_parser.h include/seqan/arg_parse/tool_doc.h include/seqan/arg_parse/xml_support.h @@ -137,7 +159,6 @@ include/seqan/basic/basic_math.h include/seqan/basic/basic_metaprogramming.h include/seqan/basic/basic_parallelism.h include/seqan/basic/basic_proxy.h -include/seqan/basic/basic_simd_vector.h include/seqan/basic/basic_smart_pointer.h include/seqan/basic/basic_stream.h include/seqan/basic/basic_tangle.h @@ -267,6 +288,7 @@ include/seqan/graph_algorithms/graph_algorithm_heap_tree.h include/seqan/graph_algorithms/graph_algorithm_hmm.h include/seqan/graph_algorithms/graph_algorithm_lis_his.h include/seqan/graph_algorithms/kruskal.h +include/seqan/graph_algorithms/maximum_weighted_matching.h include/seqan/graph_algorithms/path_growing.h include/seqan/graph_algorithms/prim.h include/seqan/graph_algorithms/single_source_shortest_path.h @@ -326,6 +348,7 @@ include/seqan/index/find2_backtracking.h include/seqan/index/find2_base.h include/seqan/index/find2_functors.h include/seqan/index/find2_index.h +include/seqan/index/find2_index_approx.h include/seqan/index/find2_index_multi.h include/seqan/index/find2_vstree_factory.h include/seqan/index/find_backtracking.h @@ -476,6 +499,8 @@ include/seqan/modifier/modifier_shortcuts.h include/seqan/modifier/modifier_string.h include/seqan/modifier/modifier_view.h include/seqan/parallel.h +include/seqan/parallel/enumerable_thread_local.h +include/seqan/parallel/enumerable_thread_local_iterator.h include/seqan/parallel/parallel_algorithms.h include/seqan/parallel/parallel_atomic_misc.h include/seqan/parallel/parallel_atomic_primitives.h @@ -488,6 +513,7 @@ include/seqan/parallel/parallel_sequence.h include/seqan/parallel/parallel_serializer.h include/seqan/parallel/parallel_splitting.h include/seqan/parallel/parallel_tags.h +include/seqan/parallel/parallel_thread_pool.h include/seqan/parse_lm.h include/seqan/parse_lm/local_match_store.h include/seqan/parse_lm/parse_blastn_tabular.h @@ -521,12 +547,33 @@ include/seqan/realign/realign_helper_functions.h include/seqan/reduced_aminoacid.h include/seqan/reduced_aminoacid/reduced_aminoacid_base.h include/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h +include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_base.h +include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_tables.h +include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_base.h +include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_tables.h include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h +include/seqan/reduced_aminoacid/reduced_aminoacid_li10_base.h +include/seqan/reduced_aminoacid/reduced_aminoacid_li10_tables.h include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h +include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_base.h +include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_tables.h +include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_base.h +include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_tables.h +include/seqan/rna_io.h +include/seqan/rna_io/bpseq_read_write.h +include/seqan/rna_io/connect_read_write.h +include/seqan/rna_io/dot_bracket_read_write.h +include/seqan/rna_io/ebpseq_read_write.h +include/seqan/rna_io/rna_header.h +include/seqan/rna_io/rna_io_context.h +include/seqan/rna_io/rna_record.h +include/seqan/rna_io/rna_struct_file.h +include/seqan/rna_io/stockholm_read_write.h +include/seqan/rna_io/vienna_read_write.h include/seqan/roi_io.h include/seqan/roi_io/read_roi.h include/seqan/roi_io/roi_file.h @@ -564,6 +611,7 @@ include/seqan/seeds/seeds_seed_set_scored.h include/seqan/seeds/seeds_seed_set_unordered.h include/seqan/seeds/seeds_seed_simple.h include/seqan/seq_io.h +include/seqan/seq_io/bam_sam.h include/seqan/seq_io/fai_index.h include/seqan/seq_io/fasta_fastq.h include/seqan/seq_io/genomic_region.h @@ -606,6 +654,14 @@ include/seqan/sequence_journaled/journal_entry.h include/seqan/sequence_journaled/sequence_journaled.h include/seqan/sequence_journaled/sequence_journaled_iterator.h include/seqan/sequence_journaled/sequence_journaled_iterator_fast.h +include/seqan/simd.h +include/seqan/simd/simd_base.h +include/seqan/simd/simd_base_seqan_impl.h +include/seqan/simd/simd_base_seqan_impl_avx2.h +include/seqan/simd/simd_base_seqan_impl_avx512.h +include/seqan/simd/simd_base_seqan_impl_sse4.2.h +include/seqan/simd/simd_base_seqan_interface.h +include/seqan/simd/simd_base_umesimd_impl.h include/seqan/simple_intervals_io.h include/seqan/simple_intervals_io/simple_intervals_file.h include/seqan/simple_intervals_io/simple_intervals_io.h @@ -671,1243 +727,5 @@ include/seqan/vcf_io/vcf_io_context.h include/seqan/vcf_io/vcf_record.h include/seqan/vcf_io/write_vcf.h include/seqan/version.h +lib/cmake/seqan/seqan-config.cmake libdata/pkgconfig/seqan-2.pc -share/cmake/Modules/FindSeqAn.cmake -%%PORTDOCS%%%%DOCSDIR%%/CHANGELOG.rst -%%PORTDOCS%%%%DOCSDIR%%/LICENSE -%%PORTDOCS%%%%DOCSDIR%%/README.rst -%%PORTDOCS%%%%DOCSDIR%%/html/class_AFScore.html -%%PORTDOCS%%%%DOCSDIR%%/html/class_Accumulator.html -%%PORTDOCS%%%%DOCSDIR%%/html/class_Align.html 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