diff options
| author | amdmi3 <amdmi3@FreeBSD.org> | 2012-06-07 01:51:33 +0800 |
|---|---|---|
| committer | amdmi3 <amdmi3@FreeBSD.org> | 2012-06-07 01:51:33 +0800 |
| commit | 479ccb63746e20cb25c30fb2721f2554ac6ff0c1 (patch) | |
| tree | 15da726c18fdf3595b863189164974b274671683 /biology | |
| parent | 26fd96059b8e435872d7a2e803dfe096b3abb2a1 (diff) | |
| download | freebsd-ports-gnome-479ccb63746e20cb25c30fb2721f2554ac6ff0c1.tar.gz freebsd-ports-gnome-479ccb63746e20cb25c30fb2721f2554ac6ff0c1.tar.zst freebsd-ports-gnome-479ccb63746e20cb25c30fb2721f2554ac6ff0c1.zip | |
SeqAn is an open source C++ library of efficient algorithms
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.
WWW: http://www.seqan.de/
PR: 167571
Submitted by: Hannes <h2+fbsdports@fsfe.org>
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/seqan/Makefile | 49 | ||||
| -rw-r--r-- | biology/seqan/distinfo | 2 | ||||
| -rw-r--r-- | biology/seqan/files/patch-cmake-CMakeLists.txt | 13 | ||||
| -rw-r--r-- | biology/seqan/files/patch-cmake-apps-CMakeLists.txt | 8 | ||||
| -rw-r--r-- | biology/seqan/files/pkg-message.in | 6 | ||||
| -rw-r--r-- | biology/seqan/pkg-descr | 6 | ||||
| -rw-r--r-- | biology/seqan/pkg-plist | 2145 |
8 files changed, 2230 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 5df882f719d5..3134c5ddf4d0 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -85,6 +85,7 @@ SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += seaview + SUBDIR += seqan SUBDIR += seqio SUBDIR += sim4 SUBDIR += ssaha diff --git a/biology/seqan/Makefile b/biology/seqan/Makefile new file mode 100644 index 000000000000..96675e464607 --- /dev/null +++ b/biology/seqan/Makefile @@ -0,0 +1,49 @@ +# New ports collection makefile for: seqan +# Date created: 3 May 2012 +# Whom: h2 +# +# $FreeBSD$ +# + +PORTNAME= seqan +PORTVERSION= 1.3.1 +CATEGORIES= biology +MASTER_SITES= http://ftp.seqan.de/releases/ + +MAINTAINER= h2+fsbdports@fsfe.org +COMMENT= C++ Sequence Analysis Library + +LICENSE= BSD GPLv3 +LICENSE_COMB= multi + +LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE +LICENSE_FILE_GPLv3=${WRKSRC}/apps/LICENSE + +USE_ZIP= yes + +USE_CMAKE= yes +CMAKE_SOURCE_PATH=${WRKSRC}/cmake +CMAKE_OUTSOURCE=yes +USE_PYTHON_BUILD=yes +MAKE_JOB_SAFE= yes + +SUB_FILES= pkg-message +PKG_MESSAGE= ${WRKDIR}/pkg-message + +.include <bsd.port.pre.mk> + +.if ${ARCH} == i386 +# triggers internal error in system gcc +USE_GCC= 4.4+ +.endif + +# unsafe workaround because FreeBSD lacks logl and expl +# see "BUGS" in `man 3 math` +post-patch: + @${REINPLACE_CMD} -e 's|expl|exp|g' ${WRKSRC}/apps/snp_store/snp_store.h + @${REINPLACE_CMD} -e 's|logl|log|g' ${WRKSRC}/apps/snp_store/snp_store.h + +post-install: + @${CAT} ${PKG_MESSAGE} + +.include <bsd.port.post.mk> diff --git a/biology/seqan/distinfo b/biology/seqan/distinfo new file mode 100644 index 000000000000..3e7a0a49d7b4 --- /dev/null +++ b/biology/seqan/distinfo @@ -0,0 +1,2 @@ +SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb +SIZE (seqan-1.3.1.zip) = 8787521 diff --git a/biology/seqan/files/patch-cmake-CMakeLists.txt b/biology/seqan/files/patch-cmake-CMakeLists.txt new file mode 100644 index 000000000000..8f39eebd62f6 --- /dev/null +++ b/biology/seqan/files/patch-cmake-CMakeLists.txt @@ -0,0 +1,13 @@ +--- cmake/CMakeLists.txt.orig 2012-05-04 12:56:23.000000000 +0800 ++++ cmake/CMakeLists.txt 2012-05-04 13:00:03.000000000 +0800 +@@ -146,6 +146,10 @@ + COMPONENT headers) + #message("install(FILES ${HEADER} RENAME seqan${NEW_PATH} DESTINATION include COMPONENT headers)") + endforeach() ++#seqan.h ++install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../seqan.h ++ DESTINATION include ++ COMPONENT headers) + + ################################################################################ + # Set Compiler Flags diff --git a/biology/seqan/files/patch-cmake-apps-CMakeLists.txt b/biology/seqan/files/patch-cmake-apps-CMakeLists.txt new file mode 100644 index 000000000000..21f5acf7b97f --- /dev/null +++ b/biology/seqan/files/patch-cmake-apps-CMakeLists.txt @@ -0,0 +1,8 @@ +--- cmake/apps/CMakeLists.txt.orig 2012-05-04 11:12:35.000000000 +0800 ++++ cmake/apps/CMakeLists.txt 2012-05-04 11:23:26.000000000 +0800 +@@ -108,4 +108,4 @@ + + # Install RazerS gapped parameters. + install(DIRECTORY ${SEQAN_LIBRARY}/apps/razers2/gapped_params +- DESTINATION bin) ++ DESTINATION share/seqan) diff --git a/biology/seqan/files/pkg-message.in b/biology/seqan/files/pkg-message.in new file mode 100644 index 000000000000..71fbb10d6371 --- /dev/null +++ b/biology/seqan/files/pkg-message.in @@ -0,0 +1,6 @@ +gapped_params for Razers2 have been installed to + %%PREFIX%%/share/seqan/gapped_params + +If you require these, make sure to set the correct +path with --param-dir as Razers2 will not pick them +up automatically. diff --git a/biology/seqan/pkg-descr b/biology/seqan/pkg-descr new file mode 100644 index 000000000000..298ab519446f --- /dev/null +++ b/biology/seqan/pkg-descr @@ -0,0 +1,6 @@ +SeqAn is an open source C++ library of efficient algorithms +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. + +WWW: http://www.seqan.de/ diff --git a/biology/seqan/pkg-plist b/biology/seqan/pkg-plist new file mode 100644 index 000000000000..94398b23eb8c --- /dev/null +++ b/biology/seqan/pkg-plist @@ -0,0 +1,2145 @@ +bin/dfi +bin/insegt +bin/mason +bin/micro_razers +bin/pair_align +bin/param_chooser +bin/rabema +bin/razers +bin/razers2 +bin/rep_sep +bin/sak +bin/seqan_tcoffee +bin/seqcons +bin/snp_store +bin/splazers +bin/stellar +bin/tree_recon +include/seqan.h +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 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