From owner-svn-ports-head@freebsd.org Sat Apr 21 17:21:32 2018 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id B4203FB4786; Sat, 21 Apr 2018 17:21:31 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 5D309818E1; Sat, 21 Apr 2018 17:21:31 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 5804B1D40; Sat, 21 Apr 2018 17:21:31 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w3LHLVu0064709; Sat, 21 Apr 2018 17:21:31 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w3LHLUY4064704; Sat, 21 Apr 2018 17:21:30 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <201804211721.w3LHLUY4064704@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Sat, 21 Apr 2018 17:21:30 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r467901 - in head/biology: . pbseqan X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . pbseqan X-SVN-Commit-Revision: 467901 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 21 Apr 2018 17:21:32 -0000 Author: jwb Date: Sat Apr 21 17:21:30 2018 New Revision: 467901 URL: https://svnweb.freebsd.org/changeset/ports/467901 Log: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15152 Added: head/biology/pbseqan/ head/biology/pbseqan/Makefile (contents, props changed) head/biology/pbseqan/distinfo (contents, props changed) head/biology/pbseqan/pkg-descr (contents, props changed) head/biology/pbseqan/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Apr 21 16:45:25 2018 (r467900) +++ head/biology/Makefile Sat Apr 21 17:21:30 2018 (r467901) @@ -81,6 +81,7 @@ SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml + SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred Added: head/biology/pbseqan/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbseqan/Makefile Sat Apr 21 17:21:30 2018 (r467901) @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= pbseqan +DISTVERSION= g20171002 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Pacific Biosciences patched and stripped down SeqAn + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +USE_GITHUB= yes +GH_ACCOUNT= PacificBiosciences +GH_PROJECT= seqan +GH_TAGNAME= d01138731be5d54ef4948053493408075f19e0b1 + +NO_BUILD= yes +NO_ARCH= yes + +do-install: + ${MKDIR} ${STAGEDIR}${PREFIX}/include/PacBio + cd ${WRKSRC}/include/seqan && \ + ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include/PacBio/seqan + +.include Added: head/biology/pbseqan/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbseqan/distinfo Sat Apr 21 17:21:30 2018 (r467901) @@ -0,0 +1,3 @@ +TIMESTAMP = 1524324484 +SHA256 (PacificBiosciences-seqan-g20171002-d01138731be5d54ef4948053493408075f19e0b1_GH0.tar.gz) = c17d3935405a3282b59ae30e4bcc8e1e690342318aa8e46257a52b2704b92460 +SIZE (PacificBiosciences-seqan-g20171002-d01138731be5d54ef4948053493408075f19e0b1_GH0.tar.gz) = 1527074 Added: head/biology/pbseqan/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbseqan/pkg-descr Sat Apr 21 17:21:30 2018 (r467901) @@ -0,0 +1,11 @@ +This is a public fork of the SeqAn Library v2.0.0, stripped down to just the +header files and with a few custom fixes. + +Some of PacBio's tools depend on SeqAn for efficient implementations of some +common data-structures for sequence analysis (A huge thanks to SeqAn +development team!). However PacBio only uses a small amount of the SeqAn +code-base, and in addition requires a few minor fixes that didn't make it in to +the initial release of SeqAn v2.0.0. Thus to minimize confusion and band-width, +we will depend on this fork instead of SeqAn proper. + +WWW: https://github.com/PacificBiosciences/seqan Added: head/biology/pbseqan/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbseqan/pkg-plist Sat Apr 21 17:21:30 2018 (r467901) @@ -0,0 +1,657 @@ +include/PacBio/seqan/LICENSE +include/PacBio/seqan/align.h +include/PacBio/seqan/align/align_base.h +include/PacBio/seqan/align/align_cols.h +include/PacBio/seqan/align/align_config.h +include/PacBio/seqan/align/align_iterator_base.h +include/PacBio/seqan/align/align_metafunctions.h +include/PacBio/seqan/align/align_traceback.h +include/PacBio/seqan/align/alignment_algorithm_tags.h +include/PacBio/seqan/align/alignment_operations.h +include/PacBio/seqan/align/dp_algorithm_impl.h +include/PacBio/seqan/align/dp_band.h +include/PacBio/seqan/align/dp_cell.h +include/PacBio/seqan/align/dp_cell_affine.h +include/PacBio/seqan/align/dp_cell_dynamic.h +include/PacBio/seqan/align/dp_cell_linear.h +include/PacBio/seqan/align/dp_context.h +include/PacBio/seqan/align/dp_formula.h +include/PacBio/seqan/align/dp_formula_affine.h +include/PacBio/seqan/align/dp_formula_dynamic.h +include/PacBio/seqan/align/dp_formula_linear.h +include/PacBio/seqan/align/dp_matrix.h +include/PacBio/seqan/align/dp_matrix_navigator.h +include/PacBio/seqan/align/dp_matrix_navigator_score_matrix.h +include/PacBio/seqan/align/dp_matrix_navigator_score_matrix_sparse.h +include/PacBio/seqan/align/dp_matrix_navigator_trace_matrix.h +include/PacBio/seqan/align/dp_matrix_sparse.h +include/PacBio/seqan/align/dp_meta_info.h +include/PacBio/seqan/align/dp_profile.h +include/PacBio/seqan/align/dp_scout.h +include/PacBio/seqan/align/dp_setup.h +include/PacBio/seqan/align/dp_trace_segment.h +include/PacBio/seqan/align/dp_traceback_adaptor.h +include/PacBio/seqan/align/dp_traceback_impl.h +include/PacBio/seqan/align/evaluate_alignment.h +include/PacBio/seqan/align/fragment.h +include/PacBio/seqan/align/gap_anchor.h +include/PacBio/seqan/align/gapped_value_type.h +include/PacBio/seqan/align/gaps_anchor.h +include/PacBio/seqan/align/gaps_array.h +include/PacBio/seqan/align/gaps_base.h +include/PacBio/seqan/align/gaps_iterator_anchor.h +include/PacBio/seqan/align/gaps_iterator_array.h +include/PacBio/seqan/align/gaps_iterator_base.h +include/PacBio/seqan/align/global_alignment_banded.h +include/PacBio/seqan/align/global_alignment_hirschberg_impl.h +include/PacBio/seqan/align/global_alignment_myers_hirschberg_impl.h +include/PacBio/seqan/align/global_alignment_myers_impl.h +include/PacBio/seqan/align/global_alignment_specialized.h +include/PacBio/seqan/align/global_alignment_unbanded.h +include/PacBio/seqan/align/local_alignment_banded.h +include/PacBio/seqan/align/local_alignment_banded_waterman_eggert_impl.h +include/PacBio/seqan/align/local_alignment_enumeration.h +include/PacBio/seqan/align/local_alignment_enumeration_banded.h +include/PacBio/seqan/align/local_alignment_enumeration_unbanded.h +include/PacBio/seqan/align/local_alignment_unbanded.h +include/PacBio/seqan/align/local_alignment_waterman_eggert_impl.h +include/PacBio/seqan/align/matrix_base.h +include/PacBio/seqan/align_extend.h +include/PacBio/seqan/align_extend/align_extend.h +include/PacBio/seqan/align_extend/align_extend_base.h +include/PacBio/seqan/align_extend/dp_scout_xdrop.h +include/PacBio/seqan/align_profile.h +include/PacBio/seqan/align_profile/add_to_profile.h +include/PacBio/seqan/align_profile/score_profile_seq.h +include/PacBio/seqan/align_split.h +include/PacBio/seqan/align_split/align_split_interface.h +include/PacBio/seqan/align_split/dp_scout_split.h +include/PacBio/seqan/alignment_free.h +include/PacBio/seqan/alignment_free/af_d2.h +include/PacBio/seqan/alignment_free/af_d2star.h +include/PacBio/seqan/alignment_free/af_d2z.h +include/PacBio/seqan/alignment_free/af_n2.h +include/PacBio/seqan/alignment_free/alignment_free_base.h +include/PacBio/seqan/alignment_free/alignment_free_comparison.h +include/PacBio/seqan/alignment_free/kmer_functions.h +include/PacBio/seqan/arg_parse.h +include/PacBio/seqan/arg_parse/arg_parse_argument.h +include/PacBio/seqan/arg_parse/arg_parse_ctd_support.h +include/PacBio/seqan/arg_parse/arg_parse_doc.h +include/PacBio/seqan/arg_parse/arg_parse_exceptions.h +include/PacBio/seqan/arg_parse/arg_parse_option.h +include/PacBio/seqan/arg_parse/arg_parse_parse.h +include/PacBio/seqan/arg_parse/arg_parse_type_support.h +include/PacBio/seqan/arg_parse/argument_parser.h +include/PacBio/seqan/arg_parse/tool_doc.h +include/PacBio/seqan/arg_parse/xml_support.h +include/PacBio/seqan/bam_io.h +include/PacBio/seqan/bam_io/bam_alignment_record.h +include/PacBio/seqan/bam_io/bam_alignment_record_util.h +include/PacBio/seqan/bam_io/bam_file.h +include/PacBio/seqan/bam_io/bam_header_record.h +include/PacBio/seqan/bam_io/bam_index_bai.h +include/PacBio/seqan/bam_io/bam_io_context.h +include/PacBio/seqan/bam_io/bam_sam_conversion.h +include/PacBio/seqan/bam_io/bam_scanner_cache.h +include/PacBio/seqan/bam_io/bam_tags_dict.h +include/PacBio/seqan/bam_io/cigar.h +include/PacBio/seqan/bam_io/read_bam.h +include/PacBio/seqan/bam_io/read_sam.h +include/PacBio/seqan/bam_io/write_bam.h +include/PacBio/seqan/bam_io/write_sam.h +include/PacBio/seqan/basic.h +include/PacBio/seqan/basic/aggregate_concept.h +include/PacBio/seqan/basic/allocator_chunkpool.h +include/PacBio/seqan/basic/allocator_interface.h +include/PacBio/seqan/basic/allocator_multipool.h +include/PacBio/seqan/basic/allocator_simple.h +include/PacBio/seqan/basic/allocator_singlepool.h +include/PacBio/seqan/basic/allocator_to_std.h +include/PacBio/seqan/basic/alphabet_adapt_builtins.h +include/PacBio/seqan/basic/alphabet_bio.h +include/PacBio/seqan/basic/alphabet_concept.h +include/PacBio/seqan/basic/alphabet_math.h +include/PacBio/seqan/basic/alphabet_profile.h +include/PacBio/seqan/basic/alphabet_qualities.h +include/PacBio/seqan/basic/alphabet_residue.h +include/PacBio/seqan/basic/alphabet_residue_funcs.h +include/PacBio/seqan/basic/alphabet_residue_tabs.h +include/PacBio/seqan/basic/alphabet_simple_type.h +include/PacBio/seqan/basic/alphabet_storage.h +include/PacBio/seqan/basic/array_construct_destruct.h +include/PacBio/seqan/basic/basic_aggregate.h +include/PacBio/seqan/basic/basic_allocator.h +include/PacBio/seqan/basic/basic_alphabet.h +include/PacBio/seqan/basic/basic_concept.h +include/PacBio/seqan/basic/basic_container.h +include/PacBio/seqan/basic/basic_debug.h +include/PacBio/seqan/basic/basic_device.h +include/PacBio/seqan/basic/basic_exception.h +include/PacBio/seqan/basic/basic_functors.h +include/PacBio/seqan/basic/basic_fundamental.h +include/PacBio/seqan/basic/basic_iterator.h +include/PacBio/seqan/basic/basic_math.h +include/PacBio/seqan/basic/basic_metaprogramming.h +include/PacBio/seqan/basic/basic_parallelism.h +include/PacBio/seqan/basic/basic_proxy.h +include/PacBio/seqan/basic/basic_simd_vector.h +include/PacBio/seqan/basic/basic_smart_pointer.h +include/PacBio/seqan/basic/basic_stream.h +include/PacBio/seqan/basic/basic_tangle.h +include/PacBio/seqan/basic/basic_type.h +include/PacBio/seqan/basic/basic_view.h +include/PacBio/seqan/basic/boost_preprocessor_subset.h +include/PacBio/seqan/basic/builtin_functions.h +include/PacBio/seqan/basic/concept_checking.h +include/PacBio/seqan/basic/container_concept.h +include/PacBio/seqan/basic/debug_helper.h +include/PacBio/seqan/basic/debug_test_system.h +include/PacBio/seqan/basic/fundamental_chunking.h +include/PacBio/seqan/basic/fundamental_comparison.h +include/PacBio/seqan/basic/fundamental_concepts.h +include/PacBio/seqan/basic/fundamental_conversion.h +include/PacBio/seqan/basic/fundamental_metafunctions.h +include/PacBio/seqan/basic/fundamental_tags.h +include/PacBio/seqan/basic/fundamental_transport.h +include/PacBio/seqan/basic/holder_base.h +include/PacBio/seqan/basic/holder_simple.h +include/PacBio/seqan/basic/holder_tristate.h +include/PacBio/seqan/basic/hosted_type_interface.h +include/PacBio/seqan/basic/iterator_adapt_pointer.h +include/PacBio/seqan/basic/iterator_adapt_std.h +include/PacBio/seqan/basic/iterator_adaptor.h +include/PacBio/seqan/basic/iterator_base.h +include/PacBio/seqan/basic/iterator_concept.h +include/PacBio/seqan/basic/iterator_counting.h +include/PacBio/seqan/basic/iterator_interface.h +include/PacBio/seqan/basic/iterator_position.h +include/PacBio/seqan/basic/iterator_range.h +include/PacBio/seqan/basic/macro_deprecated.h +include/PacBio/seqan/basic/math_functions.h +include/PacBio/seqan/basic/math_log_space_value.h +include/PacBio/seqan/basic/metaprogramming_control.h +include/PacBio/seqan/basic/metaprogramming_enable_if.h +include/PacBio/seqan/basic/metaprogramming_logic.h +include/PacBio/seqan/basic/metaprogramming_math.h +include/PacBio/seqan/basic/metaprogramming_type.h +include/PacBio/seqan/basic/metaprogramming_type_algebra.h +include/PacBio/seqan/basic/pair_base.h +include/PacBio/seqan/basic/pair_bit_compressed.h +include/PacBio/seqan/basic/pair_packed.h +include/PacBio/seqan/basic/profiling.h +include/PacBio/seqan/basic/property_map_concept.h +include/PacBio/seqan/basic/proxy_base.h +include/PacBio/seqan/basic/proxy_iterator.h +include/PacBio/seqan/basic/test_system.h +include/PacBio/seqan/basic/triple_base.h +include/PacBio/seqan/basic/triple_packed.h +include/PacBio/seqan/basic/tuple_base.h +include/PacBio/seqan/basic/tuple_bit_compressed.h +include/PacBio/seqan/basic/volatile_ptr.h +include/PacBio/seqan/bed_io.h +include/PacBio/seqan/bed_io/bed_file.h +include/PacBio/seqan/bed_io/bed_record.h +include/PacBio/seqan/bed_io/read_bed.h +include/PacBio/seqan/bed_io/write_bed.h +include/PacBio/seqan/consensus.h +include/PacBio/seqan/consensus/consensus_aligner.h +include/PacBio/seqan/consensus/consensus_aligner_interface.h +include/PacBio/seqan/consensus/consensus_alignment_options.h +include/PacBio/seqan/consensus/consensus_base.h +include/PacBio/seqan/consensus/consensus_builder.h +include/PacBio/seqan/consensus/consensus_library.h +include/PacBio/seqan/consensus/consensus_realign.h +include/PacBio/seqan/consensus/consensus_score.h +include/PacBio/seqan/consensus/overlap_info_computation.h +include/PacBio/seqan/consensus/overlapper.h +include/PacBio/seqan/file.h +include/PacBio/seqan/file/file_base.h +include/PacBio/seqan/file/file_cstyle.h +include/PacBio/seqan/file/file_forwards.h +include/PacBio/seqan/file/file_interface.h +include/PacBio/seqan/file/file_mapping.h +include/PacBio/seqan/file/file_page.h +include/PacBio/seqan/file/string_external.h +include/PacBio/seqan/file/string_mmap.h +include/PacBio/seqan/find.h +include/PacBio/seqan/find/find_abndm.h +include/PacBio/seqan/find/find_ahocorasick.h +include/PacBio/seqan/find/find_base.h +include/PacBio/seqan/find/find_begin.h +include/PacBio/seqan/find/find_bndm.h +include/PacBio/seqan/find/find_bom.h +include/PacBio/seqan/find/find_hamming_simple.h +include/PacBio/seqan/find/find_horspool.h +include/PacBio/seqan/find/find_lambda.h +include/PacBio/seqan/find/find_multi.h +include/PacBio/seqan/find/find_multiple_bfam.h +include/PacBio/seqan/find/find_multiple_shiftand.h +include/PacBio/seqan/find/find_myers_ukkonen.h +include/PacBio/seqan/find/find_pattern_base.h +include/PacBio/seqan/find/find_pex.h +include/PacBio/seqan/find/find_score.h +include/PacBio/seqan/find/find_set_horspool.h +include/PacBio/seqan/find/find_shiftand.h +include/PacBio/seqan/find/find_shiftor.h +include/PacBio/seqan/find/find_simple.h +include/PacBio/seqan/find/find_wild_shiftand.h +include/PacBio/seqan/find/find_wumanber.h +include/PacBio/seqan/gff_io.h +include/PacBio/seqan/gff_io/gff_file.h +include/PacBio/seqan/gff_io/gff_io_base.h +include/PacBio/seqan/graph_algorithms.h +include/PacBio/seqan/graph_algorithms/all_pairs_shortest_path.h +include/PacBio/seqan/graph_algorithms/bellman_ford.h +include/PacBio/seqan/graph_algorithms/bipartite_matching.h +include/PacBio/seqan/graph_algorithms/breadth_first_search.h +include/PacBio/seqan/graph_algorithms/connected_components.h +include/PacBio/seqan/graph_algorithms/depth_first_search.h +include/PacBio/seqan/graph_algorithms/dijkstra.h +include/PacBio/seqan/graph_algorithms/floyd_warshall.h +include/PacBio/seqan/graph_algorithms/ford_fulkerson.h +include/PacBio/seqan/graph_algorithms/graph_algorithm_heap_tree.h +include/PacBio/seqan/graph_algorithms/graph_algorithm_hmm.h +include/PacBio/seqan/graph_algorithms/graph_algorithm_lis_his.h +include/PacBio/seqan/graph_algorithms/kruskal.h +include/PacBio/seqan/graph_algorithms/path_growing.h +include/PacBio/seqan/graph_algorithms/prim.h +include/PacBio/seqan/graph_algorithms/single_source_shortest_path.h +include/PacBio/seqan/graph_algorithms/strongly_connected_compnents.h +include/PacBio/seqan/graph_algorithms/topological_sort.h +include/PacBio/seqan/graph_algorithms/transitive_closure.h +include/PacBio/seqan/graph_algorithms/weakly_connected_components.h +include/PacBio/seqan/graph_algorithms/weighted_bipartite_matching.h +include/PacBio/seqan/graph_align.h +include/PacBio/seqan/graph_align/graph_algorithm_refine_align.h +include/PacBio/seqan/graph_align/graph_algorithm_refine_aligngraph.h +include/PacBio/seqan/graph_align/graph_algorithm_refine_annotation.h +include/PacBio/seqan/graph_align/graph_algorithm_refine_exact.h +include/PacBio/seqan/graph_align/graph_algorithm_refine_exact_iterative.h +include/PacBio/seqan/graph_align/graph_algorithm_refine_fragment.h +include/PacBio/seqan/graph_align/graph_algorithm_refine_inexact.h +include/PacBio/seqan/graph_align/graph_algorithm_refine_scoring.h 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