diff options
| author | Jason Unovitch <junovitch@FreeBSD.org> | 2016-05-10 01:05:23 +0000 |
|---|---|---|
| committer | Jason Unovitch <junovitch@FreeBSD.org> | 2016-05-10 01:05:23 +0000 |
| commit | 864e413d06720ad83d6fbcb852ef248273f383b3 (patch) | |
| tree | bf7834fa76062f3aa36e5f11b8f645c53a7532d5 /biology/seqan1 | |
| parent | 7a3991c9de3e68056b7b5d0b8631f774cf2a78b0 (diff) | |
| download | ports-864e413d06720ad83d6fbcb852ef248273f383b3.tar.gz ports-864e413d06720ad83d6fbcb852ef248273f383b3.zip | |
biology/seqan: update 1.3.1 -> 2.1.1
biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage
PR: 204127
Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
Notes
Notes:
svn path=/head/; revision=414898
Diffstat (limited to 'biology/seqan1')
| -rw-r--r-- | biology/seqan1/Makefile | 31 | ||||
| -rw-r--r-- | biology/seqan1/distinfo | 2 | ||||
| -rw-r--r-- | biology/seqan1/pkg-descr | 10 | ||||
| -rw-r--r-- | biology/seqan1/pkg-plist | 1983 |
4 files changed, 2026 insertions, 0 deletions
diff --git a/biology/seqan1/Makefile b/biology/seqan1/Makefile new file mode 100644 index 000000000000..d5222cac07b2 --- /dev/null +++ b/biology/seqan1/Makefile @@ -0,0 +1,31 @@ +# Created by: h2 +# $FreeBSD$ + +PORTNAME= seqan +PORTVERSION= 1.3.1 +PORTREVISION= 3 +CATEGORIES= biology +MASTER_SITES= http://ftp.seqan.de/releases/ +PKGNAMESUFFIX= 1 + +MAINTAINER= h2+fbsdports@fsfe.org +COMMENT= C++ Sequence Analysis Library + +LICENSE= BSD3CLAUSE +LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE + +USES= zip +NO_BUILD= yes + +CONFLICTS= seqan-[2-9]* + +do-install: + ${MKDIR} ${STAGEDIR}/${PREFIX}/include/${PORTNAME} + cd ${WRKSRC} && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include + cd ${WRKSRC} && ${INSTALL_DATA} ./${PORTNAME}.h ${STAGEDIR}/${PREFIX}/include + +post-install: + ${MKDIR} ${STAGEDIR}${DOCSDIR} + cd ${WRKSRC}/docs && ${COPYTREE_SHARE} ./ ${STAGEDIR}${DOCSDIR} + +.include <bsd.port.mk> diff --git a/biology/seqan1/distinfo b/biology/seqan1/distinfo new file mode 100644 index 000000000000..3e7a0a49d7b4 --- /dev/null +++ b/biology/seqan1/distinfo @@ -0,0 +1,2 @@ +SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb +SIZE (seqan-1.3.1.zip) = 8787521 diff --git a/biology/seqan1/pkg-descr b/biology/seqan1/pkg-descr new file mode 100644 index 000000000000..5f27809a1ba8 --- /dev/null +++ b/biology/seqan1/pkg-descr @@ -0,0 +1,10 @@ +SeqAn is an open source C++ library of efficient algorithms +and data structures for the analysis of sequences with the +focus on biological data. + +This port includes only the library, the apps have been +moved to biology/seqan-apps. This is the last release of +the version 1 API, it is highly recommended to upgrade to +biology/seqan (version 2). + +WWW: http://www.seqan.de/ diff --git a/biology/seqan1/pkg-plist b/biology/seqan1/pkg-plist new file mode 100644 index 000000000000..e6c2faed81f0 --- /dev/null +++ b/biology/seqan1/pkg-plist @@ -0,0 +1,1983 @@ +include/seqan.h +include/seqan/LICENSE +include/seqan/align.h +include/seqan/align/align_algorithms.h +include/seqan/align/align_base.h +include/seqan/align/align_cols_base.h +include/seqan/align/align_dynprog.h +include/seqan/align/align_generated_forwards.h +include/seqan/align/align_hirschberg.h +include/seqan/align/align_iterator_base.h +include/seqan/align/align_local_dynprog.h +include/seqan/align/align_local_dynprog_banded.h +include/seqan/align/align_myers.h +include/seqan/align/align_trace.h +include/seqan/align/gaps_array.h +include/seqan/align/gaps_base.h +include/seqan/align/gaps_iterator_base.h +include/seqan/align/gaps_sumlist.h +include/seqan/align/hirschberg_set.h +include/seqan/align/matrix_base.h +include/seqan/basic.h +include/seqan/basic/basic_aggregates.h +include/seqan/basic/basic_allocator_chunkpool.h +include/seqan/basic/basic_allocator_interface.h +include/seqan/basic/basic_allocator_multipool.h +include/seqan/basic/basic_allocator_simple.h +include/seqan/basic/basic_allocator_singlepool.h +include/seqan/basic/basic_allocator_to_std.h +include/seqan/basic/basic_alphabet_interface.h +include/seqan/basic/basic_alphabet_interface2.h +include/seqan/basic/basic_alphabet_simple.h +include/seqan/basic/basic_alphabet_simple_tabs.h +include/seqan/basic/basic_alphabet_trait_basic.h +include/seqan/basic/basic_compare.h +include/seqan/basic/basic_converter.h +include/seqan/basic/basic_counted_ptr.h +include/seqan/basic/basic_debug.h +include/seqan/basic/basic_definition.h +include/seqan/basic/basic_forwards.h +include/seqan/basic/basic_generated_forwards.h +include/seqan/basic/basic_holder.h +include/seqan/basic/basic_holder_dynamic.h +include/seqan/basic/basic_host.h +include/seqan/basic/basic_iterator.h +include/seqan/basic/basic_iterator_adapt_std.h +include/seqan/basic/basic_iterator_adaptor.h +include/seqan/basic/basic_iterator_base.h +include/seqan/basic/basic_iterator_position.h +include/seqan/basic/basic_iterator_simple.h +include/seqan/basic/basic_logvalue.h +include/seqan/basic/basic_metaprogramming.h +include/seqan/basic/basic_operator.h +include/seqan/basic/basic_parallelism.h +include/seqan/basic/basic_pointer.h +include/seqan/basic/basic_profchar.h +include/seqan/basic/basic_profile.h +include/seqan/basic/basic_proxy.h +include/seqan/basic/basic_sse2.h +include/seqan/basic/basic_tag.h +include/seqan/basic/basic_testing.h +include/seqan/basic/basic_transport.h +include/seqan/basic/basic_type.h +include/seqan/basic/basic_volatile_ptr.h +include/seqan/blast.h +include/seqan/blast/blast_base.h +include/seqan/blast/blast_generated_forwards.h +include/seqan/blast/blast_hit.h +include/seqan/blast/blast_hit_iterator.h +include/seqan/blast/blast_hsp.h +include/seqan/blast/blast_hsp_iterator.h +include/seqan/blast/blast_iterator.h +include/seqan/blast/blast_parsing.h +include/seqan/blast/blast_report.h +include/seqan/blast/blast_run.h +include/seqan/blast/blast_stream_hit.h +include/seqan/blast/blast_stream_hit_iterator.h +include/seqan/blast/blast_stream_hsp_iterator.h +include/seqan/blast/blast_stream_report.h +include/seqan/chaining.h +include/seqan/chaining/chain_base.h +include/seqan/chaining/chain_generic.h +include/seqan/chaining/chain_meta_fragment.h +include/seqan/chaining/chain_point.h +include/seqan/chaining/chain_wrapper_point.h +include/seqan/chaining/chaining_generated_forwards.h +include/seqan/chaining/fragment.h +include/seqan/chaining/geom_distribution.h +include/seqan/chaining/range_max_tree.h +include/seqan/chaining/range_tree.h +include/seqan/chaining/rmt_base.h +include/seqan/chaining/rmt_common_algos.h +include/seqan/chaining/rmt_compl_algos.h +include/seqan/chaining/rmt_def_algos.h +include/seqan/chaining/rmt_skip_base_element.h +include/seqan/chaining/rmt_skip_element.h +include/seqan/chaining/rt_base.h +include/seqan/chaining/rt_common_algos.h +include/seqan/chaining/rt_impl.h +include/seqan/chaining/rt_skip_base_element.h +include/seqan/chaining/rt_skip_element.h +include/seqan/chaining/rt_sl_base.h +include/seqan/chaining/rt_sl_compl_algos.h +include/seqan/chaining/rt_sl_def_algos.h +include/seqan/chaining/rt_sl_impl.h +include/seqan/chaining/score_chain.h +include/seqan/chaining/score_chain_sop.h +include/seqan/chaining/score_manhattan.h +include/seqan/chaining/score_zero.h +include/seqan/chaining/skip_base_element.h +include/seqan/chaining/skip_element.h +include/seqan/chaining/skip_list.h +include/seqan/chaining/skip_list_base.h +include/seqan/chaining/skip_list_dynamic.h +include/seqan/chaining/skip_list_impl.h +include/seqan/chaining/skip_list_iterator.h +include/seqan/chaining/skip_list_type.h +include/seqan/chaining/skip_pool_alloc.h +include/seqan/chaining/tree_chain.h +include/seqan/chaining/tree_chain_sop.h +include/seqan/chaining/tree_chain_utils.h +include/seqan/consensus.h +include/seqan/consensus/consensus_base.h +include/seqan/consensus/consensus_generated_forwards.h +include/seqan/consensus/consensus_library.h +include/seqan/consensus/consensus_realign.h +include/seqan/consensus/consensus_score.h +include/seqan/file.h +include/seqan/file/chunk_collector.h +include/seqan/file/cstream.h +include/seqan/file/file_array.h +include/seqan/file/file_base.h +include/seqan/file/file_cstyle.h +include/seqan/file/file_filereader.h +include/seqan/file/file_filereaderiterator.h +include/seqan/file/file_format.h +include/seqan/file/file_format_cgviz.h +include/seqan/file/file_format_embl.h +include/seqan/file/file_format_fasta.h +include/seqan/file/file_format_fasta_align.h +include/seqan/file/file_format_genbank.h +include/seqan/file/file_format_guess.h +include/seqan/file/file_format_mmap.h +include/seqan/file/file_format_raw.h +include/seqan/file/file_forwards.h +include/seqan/file/file_generated_forwards.h +include/seqan/file/file_page.h +include/seqan/file/file_page_raid0.h +include/seqan/file/meta.h +include/seqan/file/stream.h +include/seqan/file/stream_algorithms.h +include/seqan/file/string_external.h +include/seqan/file/string_mmap.h +include/seqan/find.h +include/seqan/find/find_abndm.h +include/seqan/find/find_ahocorasick.h +include/seqan/find/find_base.h +include/seqan/find/find_begin.h +include/seqan/find/find_bndm.h +include/seqan/find/find_bom.h +include/seqan/find/find_generated_forwards.h +include/seqan/find/find_hamming_simple.h +include/seqan/find/find_horspool.h +include/seqan/find/find_multi.h +include/seqan/find/find_multiple_bfam.h +include/seqan/find/find_multiple_shiftand.h +include/seqan/find/find_myers_ukkonen.h +include/seqan/find/find_pattern_base.h +include/seqan/find/find_pex.h +include/seqan/find/find_score.h +include/seqan/find/find_set_horspool.h +include/seqan/find/find_shiftand.h +include/seqan/find/find_shiftor.h +include/seqan/find/find_simple.h +include/seqan/find/find_wild_shiftand.h +include/seqan/find/find_wumanber.h +include/seqan/find2.h +include/seqan/find2/find2_generated_forwards.h +include/seqan/find2/find_approx_dpsearch.h +include/seqan/find2/find_approx_find_begin.h +include/seqan/find2/find_base.h +include/seqan/find2/find_exact_shiftand.h +include/seqan/find2/find_exact_simple.h +include/seqan/find2/find_finder_default.h +include/seqan/find2/find_hamming_simple.h +include/seqan/find2/find_multiple_exact_simple.h +include/seqan/find2/find_pattern_wild_shiftand.h +include/seqan/find_motif.h +include/seqan/find_motif/em_algorithm.h +include/seqan/find_motif/find_motif_base.h +include/seqan/find_motif/find_motif_epatternbranching.h +include/seqan/find_motif/find_motif_generated_forwards.h +include/seqan/find_motif/find_motif_pms1.h +include/seqan/find_motif/find_motif_pmsp.h +include/seqan/find_motif/find_motif_projection.h +include/seqan/find_motif/frequency_distribution.h +include/seqan/find_motif/profile.h +include/seqan/find_motif/pseudocount_base.h +include/seqan/find_motif/pseudocount_mode_c.h +include/seqan/find_motif/pseudocount_mode_p.h +include/seqan/find_motif/sequence_model_types.h +include/seqan/graph_algorithms.h +include/seqan/graph_algorithms/graph_algorithm.h +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/graph_algorithms_generated_forwards.h +include/seqan/graph_align.h +include/seqan/graph_align/graph_align_banded_gotoh.h +include/seqan/graph_align/graph_align_banded_needleman_wunsch.h +include/seqan/graph_align/graph_align_banded_smith_waterman_clump.h +include/seqan/graph_align/graph_align_base.h +include/seqan/graph_align/graph_align_config.h +include/seqan/graph_align/graph_align_generated_forwards.h +include/seqan/graph_align/graph_align_gotoh.h +include/seqan/graph_align/graph_align_hirschberg.h +include/seqan/graph_align/graph_align_interface.h +include/seqan/graph_align/graph_align_needleman_wunsch.h +include/seqan/graph_align/graph_align_smith_waterman.h +include/seqan/graph_align/graph_align_smith_waterman_clump.h +include/seqan/graph_msa.h +include/seqan/graph_msa/graph_align_tcoffee_base.h +include/seqan/graph_msa/graph_align_tcoffee_distance.h +include/seqan/graph_msa/graph_align_tcoffee_guidetree.h +include/seqan/graph_msa/graph_align_tcoffee_io.h +include/seqan/graph_msa/graph_align_tcoffee_kmer.h +include/seqan/graph_msa/graph_align_tcoffee_library.h +include/seqan/graph_msa/graph_align_tcoffee_msa.h +include/seqan/graph_msa/graph_align_tcoffee_progressive.h +include/seqan/graph_msa/graph_align_tcoffee_refinement.h +include/seqan/graph_msa/graph_msa_generated_forwards.h +include/seqan/graph_types.h +include/seqan/graph_types/graph_base.h +include/seqan/graph_types/graph_drawing.h +include/seqan/graph_types/graph_edgestump.h +include/seqan/graph_types/graph_idmanager.h +include/seqan/graph_types/graph_impl_automaton.h +include/seqan/graph_types/graph_impl_directed.h +include/seqan/graph_types/graph_impl_fragment.h +include/seqan/graph_types/graph_impl_hmm.h +include/seqan/graph_types/graph_impl_oracle.h +include/seqan/graph_types/graph_impl_tree.h +include/seqan/graph_types/graph_impl_trie.h +include/seqan/graph_types/graph_impl_undirected.h +include/seqan/graph_types/graph_impl_wordgraph.h +include/seqan/graph_types/graph_interface.h +include/seqan/graph_types/graph_iterator.h +include/seqan/graph_types/graph_iterator_adjacency.h +include/seqan/graph_types/graph_iterator_bfs.h +include/seqan/graph_types/graph_iterator_dfs.h +include/seqan/graph_types/graph_iterator_edge.h +include/seqan/graph_types/graph_iterator_outedge.h +include/seqan/graph_types/graph_iterator_vertex.h +include/seqan/graph_types/graph_property.h +include/seqan/graph_types/graph_types_generated_forwards.h +include/seqan/graph_types/graph_utility_parsing.h +include/seqan/index.h +include/seqan/index/find_index.h +include/seqan/index/find_index_approx.h +include/seqan/index/find_index_esa.h +include/seqan/index/find_index_qgram.h +include/seqan/index/find_quasar.h +include/seqan/index/find_swift.h +include/seqan/index/index_base.h +include/seqan/index/index_bwt.h +include/seqan/index/index_childtab.h +include/seqan/index/index_dfi.h +include/seqan/index/index_esa_algs.h +include/seqan/index/index_esa_algs_multi.h +include/seqan/index/index_esa_base.h +include/seqan/index/index_esa_drawing.h +include/seqan/index/index_esa_stree.h +include/seqan/index/index_generated_forwards.h +include/seqan/index/index_lcp.h +include/seqan/index/index_lcp_tree.h +include/seqan/index/index_manual_forwards.h +include/seqan/index/index_pizzachili.h +include/seqan/index/index_pizzachili_find.h +include/seqan/index/index_pizzachili_string.h +include/seqan/index/index_qgram.h +include/seqan/index/index_qgram_openaddressing.h +include/seqan/index/index_sa_btree.h +include/seqan/index/index_sa_bwtwalk.h +include/seqan/index/index_sa_lss.h +include/seqan/index/index_sa_mm.h +include/seqan/index/index_sa_qsort.h +include/seqan/index/index_shawarma.h +include/seqan/index/index_shims.h +include/seqan/index/index_skew3.h +include/seqan/index/index_skew7.h +include/seqan/index/index_skew7_multi.h +include/seqan/index/index_wotd.h +include/seqan/index/pipe_merger3.h +include/seqan/index/pipe_merger7.h +include/seqan/index/pizzachili_api.h +include/seqan/index/pump_extender3.h +include/seqan/index/pump_extender7.h +include/seqan/index/pump_lcp_core.h +include/seqan/index/pump_separator7.h +include/seqan/index/radix.h +include/seqan/index/repeat_base.h +include/seqan/index/shape_base.h +include/seqan/index/shape_gapped.h +include/seqan/index/shape_onegapped.h +include/seqan/index/shape_predefined.h +include/seqan/index/shape_threshold.h +include/seqan/map.h +include/seqan/map/map_adapter_stl.h +include/seqan/map/map_base.h +include/seqan/map/map_chooser.h +include/seqan/map/map_generated_forwards.h +include/seqan/map/map_skiplist.h +include/seqan/map/map_vector.h +include/seqan/map/sumlist.h +include/seqan/map/sumlist_mini.h +include/seqan/map/sumlist_skip.h +include/seqan/misc/edit_environment.h +include/seqan/misc/misc_base.h +include/seqan/misc/misc_cmdparser.h +include/seqan/misc/misc_dequeue.h +include/seqan/misc/misc_generated_forwards.h +include/seqan/misc/misc_interval_tree.h +include/seqan/misc/misc_long_word.h +include/seqan/misc/misc_map.h +include/seqan/misc/misc_parsing.h +include/seqan/misc/misc_random.h +include/seqan/misc/misc_set.h +include/seqan/misc/misc_svg.h +include/seqan/misc/priority_type_base.h +include/seqan/misc/priority_type_heap.h +include/seqan/modifier.h +include/seqan/modifier/modifier_alphabet.h +include/seqan/modifier/modifier_alphabet_expansion.h +include/seqan/modifier/modifier_functors.h +include/seqan/modifier/modifier_generated_forwards.h +include/seqan/modifier/modifier_iterator.h +include/seqan/modifier/modifier_reverse.h +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/parallel_atomic_misc.h +include/seqan/parallel/parallel_atomic_primitives.h +include/seqan/parallel/parallel_generated_forwards.h +include/seqan/parallel/parallel_macros.h +include/seqan/pipe.h +include/seqan/pipe/pipe_base.h +include/seqan/pipe/pipe_caster.h +include/seqan/pipe/pipe_counter.h +include/seqan/pipe/pipe_echoer.h +include/seqan/pipe/pipe_edit_environment.h +include/seqan/pipe/pipe_filter.h +include/seqan/pipe/pipe_generated_forwards.h +include/seqan/pipe/pipe_iterator.h +include/seqan/pipe/pipe_joiner.h +include/seqan/pipe/pipe_namer.h +include/seqan/pipe/pipe_sampler.h +include/seqan/pipe/pipe_shifter.h +include/seqan/pipe/pipe_source.h +include/seqan/pipe/pipe_tupler.h +include/seqan/pipe/pool_base.h +include/seqan/pipe/pool_mapper.h +include/seqan/pipe/pool_sorter.h +include/seqan/platform.h +include/seqan/platform/platform_gcc.h +include/seqan/platform/platform_generated_forwards.h +include/seqan/platform/platform_mingw.h +include/seqan/platform/platform_solaris.h +include/seqan/platform/platform_windows.h +include/seqan/random.h +include/seqan/random/ext_MersenneTwister.h +include/seqan/random/random_base.h +include/seqan/random/random_generated_forwards.h +include/seqan/random/random_geometric.h +include/seqan/random/random_lognormal.h +include/seqan/random/random_mt19937.h +include/seqan/random/random_normal.h +include/seqan/random/random_rng_functor.h +include/seqan/random/random_shuffle.h +include/seqan/random/random_uniform.h +include/seqan/refinement.h +include/seqan/refinement/graph_algorithm_refine_align.h +include/seqan/refinement/graph_algorithm_refine_aligngraph.h +include/seqan/refinement/graph_algorithm_refine_annotation.h +include/seqan/refinement/graph_algorithm_refine_exact.h +include/seqan/refinement/graph_algorithm_refine_exact_iterative.h +include/seqan/refinement/graph_algorithm_refine_fragment.h +include/seqan/refinement/graph_algorithm_refine_inexact.h +include/seqan/refinement/graph_algorithm_refine_scoring.h +include/seqan/refinement/graph_impl_align.h +include/seqan/refinement/graph_impl_align_adapt.h +include/seqan/refinement/refinement_generated_forwards.h +include/seqan/score.h +include/seqan/score/score_base.h +include/seqan/score/score_edit.h +include/seqan/score/score_generated_forwards.h +include/seqan/score/score_matrix.h +include/seqan/score/score_matrix_data.h +include/seqan/score/score_simple.h +include/seqan/seeds.h 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