diamond
Accelerated BLAST compatible local sequence aligner.
파일 탐색기
최종 버전 다운로드 (.zip)- cmake.yml
- codeql.yml
- FUNDING.yml
- extend.cpp
- global_ranking.cpp
- global_ranking.h
- table.cpp
- banded_swipe_pipeline.cpp
- pipeline.h
- query_mapper.cpp
- query_mapper.h
- align.cpp
- align.h
- alt_hsp.cpp
- culling.cpp
- culling.h
- def.h
- extend.cpp
- extend.h
- full_db.cpp
- gapped_filter.cpp
- gapped_final.cpp
- gapped_score.cpp
- load_hits.h
- output.cpp
- reseek.cpp
- reseek.h
- target.h
- ungapped.cpp
- basic.cpp
- config.cpp
- config.h
- const.h
- hssp.cpp
- match.h
- packed_loc.h
- packed_sequence.h
- packed_transcript.h
- reduction.h
- seed.h
- sequence.h
- shape.h
- shape_config.h
- statistics.h
- translated_position.h
- value.cpp
- value.h
- aligner.h
- backtrace.cpp
- chaining.h
- diag_graph.h
- greedy_align.cpp
- hamming_ext.cpp
- smith_waterman.cpp
- cluster.h
- data.cpp
- file_array.h
- helpers.cpp
- input_buffer.h
- len_sort.cpp
- lin_index.cpp
- make_blocks.cpp
- merge.cpp
- multinode.cpp
- multinode.h
- output.cpp
- radixed_table.h
- realign.cpp
- reassign.cpp
- recluster.cpp
- search.cpp
- volume.h
- alignment.cpp
- alignment.h
- build_score.cpp
- build_score.h
- chain.cpp
- chain.h
- dna_index.cpp
- dna_index.h
- extension.cpp
- extension.h
- extension_chain.cpp
- extension_chain.h
- extension_seed_matches.cpp
- extension_seed_matches.h
- seed_set_dna.cpp
- seed_set_dna.h
- setup.cpp
- smith_watermann.cpp
- smith_watermann.h
- timer.h
- clustering_format.cpp
- clustering_variables.cpp
- clustering_variables.h
- dense.h
- lazy_disjoint_set.h
- mcl.cpp
- mcl.h
- recursive_parser.h
- sparse.h
- sparse_matrix_stream.h
- asn1.cpp
- asn1.h
- ber.h
- blastdb.cpp
- blastdb.h
- pal.cpp
- pal.h
- phr.cpp
- pin.cpp
- psq.cpp
- taxdmp.h
- volume.h
- block.cpp
- block.h
- block_wrapper.cpp
- block_wrapper.h
- fasta_file.cpp
- fasta_file.h
- parser.h
- frequent_seeds.cpp
- frequent_seeds.h
- index.cpp
- queries.cpp
- queries.h
- seed_set.cpp
- seed_set.h
- sequence_file.cpp
- sequence_file.h
- sequence_set.cpp
- sequence_set.h
- string_set.h
- taxon_list.cpp
- taxon_list.h
- taxonomy.cpp
- taxonomy.h
- taxonomy_nodes.cpp
- taxonomy_nodes.h
- double_buffer.h
- needleman_wunsch.h
- scalar.h
- smith_waterman.cpp
- traceback.h
- anchored.h
- anchored_wrapper.cpp
- banded_3frame_swipe.cpp
- banded_matrix.h
- banded_swipe.h
- cell_update.h
- config.h
- full_matrix.h
- full_swipe.h
- stat_cell.h
- swipe.h
- swipe_wrapper.cpp
- target_iterator.h
- dp.h
- flags.h
- scan_diags.cpp
- scan_diags.h
- score_profile.cpp
- score_profile.h
- score_vector.h
- score_vector_int16.h
- score_vector_int8.h
- ungapped.h
- ungapped_align.cpp
- ungapped_simd.cpp
- ungapped_simd.h
- daa_file.h
- daa_record.cpp
- daa_record.h
- daa_write.cpp
- daa_write.h
- merge.cpp
- view.cpp
- compact_array.h
- dmnd.cpp
- dmnd.h
- io.h
- record_reader.h
- task_queue.h
- njn_approx.hpp
- njn_doubletype.hpp
- njn_dynprogprob.cpp
- njn_dynprogprob.hpp
- njn_dynprogproblim.cpp
- njn_dynprogproblim.hpp
- njn_dynprogprobproto.cpp
- njn_dynprogprobproto.hpp
- njn_function.hpp
- njn_integer.hpp
- njn_ioutil.cpp
- njn_ioutil.hpp
- njn_localmaxstat.cpp
- njn_localmaxstat.hpp
- njn_localmaxstatmatrix.cpp
- njn_localmaxstatmatrix.hpp
- njn_localmaxstatutil.cpp
- njn_localmaxstatutil.hpp
- njn_matrix.hpp
- njn_memutil.hpp
- njn_random.cpp
- njn_random.hpp
- njn_root.hpp
- njn_uniform.hpp
- njn_vector.hpp
- sls_alignment_evaluer.cpp
- sls_alignment_evaluer.hpp
- sls_alp.cpp
- sls_alp.hpp
- sls_alp_data.cpp
- sls_alp_data.hpp
- sls_alp_regression.cpp
- sls_alp_regression.hpp
- sls_alp_sim.cpp
- sls_alp_sim.hpp
- sls_basic.cpp
- sls_basic.hpp
- sls_normal_distr_array.hpp
- sls_pvalues.cpp
- sls_pvalues.hpp
- atomic_wait
- barrier
- latch
- semaphore
- blast_def.h
- blast_encoding.h
- blast_export.h
- blast_filter.cpp
- blast_filter.h
- blast_message.cpp
- blast_message.h
- blast_options.h
- blast_program.h
- blast_psi.h
- blast_psi_priv.h
- blast_query_info.h
- blast_seg.cpp
- blast_seg.h
- blast_setup.h
- blast_stat.cpp
- blast_stat.h
- blastn_score.cpp
- boost_erf.h
- matrix_freq_ratios.c
- matrix_freq_ratios.h
- ncbi_math.h
- ncbi_std.cpp
- ncbi_std.h
- ncbitype.h
- nlm_linear_algebra.cpp
- nlm_linear_algebra.h
- raw_scoremat.h
- sm_blosum45.c
- sm_blosum50.c
- sm_blosum62.c
- sm_blosum80.c
- sm_blosum90.c
- sm_pam250.c
- sm_pam30.c
- sm_pam70.c
- gsl.h
- interval_tree.hpp
- interval_tree_fwd.hpp
- interval_types.hpp
- base_case.hpp
- block_permutation.hpp
- bucket_pointers.hpp
- buffers.hpp
- classifier.hpp
- cleanup_margins.hpp
- config.hpp
- empty_block_movement.hpp
- ips4o.hpp
- ips4o_fwd.hpp
- local_classification.hpp
- memory.hpp
- parallel.hpp
- partitioning.hpp
- sampling.hpp
- sequential.hpp
- synchronization.hpp
- thread_pool.hpp
- utils.hpp
- mmap.ipp
- string_util.hpp
- forward.h
- mmap.hpp
- page.hpp
- shared_mmap.hpp
- MurmurHash3.cpp
- MurmurHash3.h
- builtin.h
- endian.h
- COPYING.txt
- LambdaCalculator.cc
- LambdaCalculator.hh
- def.h
- lambda.cpp
- masking.cpp
- masking.h
- motifs.cpp
- tantan.cpp
- tantan.h
- blast_pairwise_format.cpp
- blast_tab_format.cpp
- def.h
- join_blocks.cpp
- output.h
- output_format.cpp
- output_format.h
- output_sink.cpp
- paf_format.cpp
- sam_format.cpp
- target_culling.cpp
- target_culling.h
- taxon_format.cpp
- xml_format.cpp
- config.cpp
- config.h
- double_indexed.cpp
- main.cpp
- tools.cpp
- workflow.h
- finger_print.h
- hit_field.h
- kernel.h
- kernel_lin.h
- kernel_mutual_cov.h
- kernel_self.h
- stage1_2.cpp
- lin_index.cpp
- lin_index.h
- scan.cpp
- enum_seeds.h
- flags.h
- seed_array.cpp
- seed_array.h
- seed_array_extra.cpp
- seed_array_impl.h
- seed_histogram.cpp
- seed_histogram.h
- seed_iterator.h
- hit.h
- hit_buffer.cpp
- hit_buffer.h
- kmer_ranking.cpp
- kmer_ranking.h
- left_most.h
- search.h
- seed_complexity.cpp
- seed_complexity.h
- setup.cpp
- sse_dist.h
- stage0.cpp
- stage2.h
- blosum45.h
- blosum50.h
- blosum62.h
- blosum80.h
- blosum90.h
- pam250.h
- pam30.h
- pam70.h
- kernel_arm64.h
- kernel_avx2.h
- kernel_sse41.h
- linear_algebra_ncbi.h
- matrix_adjust.cpp
- matrix_adjust_scalar.cpp
- matrix_adjust_wrapper.cpp
- ncbi.cpp
- cbs.cpp
- cbs.h
- comp_based_stats.cpp
- hauser_correction.cpp
- hauser_correction.h
- score_matrix.cpp
- score_matrix.h
- standard_matrix.h
- stats.cpp
- stats.h
- nr_10k.pdb
- nr_10k.phr
- nr_10k.pin
- nr_10k.pjs
- nr_10k.pog
- nr_10k.pos
- nr_10k.pot
- nr_10k.psq
- nr_10k.ptf
- nr_10k.pto
- nr_10k_filtered.pal
- seqidlist.txt
- db.dmnd
- nucleotide.fasta
- 1.faa
- 2.faa
- 3.faa
- 4.faa
- 5.faa
- acc2taxid.tsv
- blastp-blocked.out
- blastp-cbs6.out
- blastp-daa.out
- blastp-f0.out
- blastp-global-ranking.out
- blastp-mid-sens.out
- blastp.out
- blastp_blastaliasdb_seqidlist.out
- blastp_blastdb.out
- blastp_nr10k.out
- blastx-nanopore-fna.out
- blastx-nanopore.out
- data.dmnd
- data.faa
- deepclust-multiblock.out
- deepclust.out
- diamond-test-blastp-blocked.out
- diamond-test-blastp-blosum50.out
- diamond-test-blastp-comp-based-stats-0.out
- diamond-test-blastp-comp-based-stats-2.out
- diamond-test-blastp-comp-based-stats-3.out
- diamond-test-blastp-comp-based-stats-4.out
- diamond-test-blastp-default.out
- diamond-test-blastp-evalue.out
- diamond-test-blastp-max-hsps.out
- diamond-test-blastp-more-sensitive.out
- diamond-test-blastp-multithreaded.out
- diamond-test-blastp-paf-format.out
- diamond-test-blastp-pairwise-format.out
- diamond-test-blastp-query-indexed.out
- diamond-test-blastp-target-parallel.out
- diamond-test-blastp-target-seqs.out
- diamond-test-blastp-top.out
- diamond-test-blastp-ultra-sensitive.out
- diamond-test-blastp-very-sensitive.out
- galaxy_7.out
- galaxy_9.out
- greedy_vertex_cover_numeric.out
- greedy_vertex_cover_numeric.tsv
- hit_buffer_stress.cpp
- linclust.out
- mini_names.dmp
- mini_nodes.dmp
- nr_10k.faa
- nr_10k.taxids.tsv
- nr_300.faa
- queue.cpp
- realign.out
- SRR14011045_1.fastq
- SRR14011045_1.fna.gz
- test.cmake
- test.cpp
- test.daa
- test.ps1
- test_exit_code.cmake
- view.out
- benchmark.cpp
- benchmark_swipe.cpp
- composition_matrix.cpp
- greedy_vertex_cover.cpp
- tools.cpp
- tools.h
- aho_corasick.h
- algo.h
- binary_search.h
- degree_partition.h
- external_sort.h
- hash.h
- hash_join.h
- hyperloglog.h
- join_result.h
- merge_files.h
- merge_sort.h
- partition.h
- pattern_matcher.h
- radix_cluster.h
- radix_sort.h
- sort.h
- sort_helper.h
- transform_iterator.h
- varint.h
- array.h
- bit_vector.h
- deque.h
- disjoint_set.h
- double_array.h
- flat_array.h
- growable_buffer.h
- hash_set.h
- hash_table.h
- mem_buffer.h
- queue.h
- range_partition.h
- reorder_queue.h
- sparse_flat_array.h
- diagonal_segment.h
- geo.h
- hit.h
- interval.h
- interval_partition.h
- interval_tree.h
- approx_hsp.h
- compressed_buffer.cpp
- compressed_buffer.h
- compressor.h
- decompressor.h
- file.cpp
- file.h
- read_text_mt.cpp
- zlib_bridge.cpp
- zstd_bridge.cpp
- kmer.h
- integer.h
- log2_fast.h
- math.h
- alignment.h
- memory_resource.h
- vmbuffer.h
- option.h
- atomic.h
- filestack.cpp
- filestack.h
- multiprocessing.cpp
- multiprocessing.h
- mutex.h
- parallelizer.cpp
- parallelizer.h
- semaphore.h
- simple_thread_pool.h
- thread_pool.h
- cutoff_table.h
- seed_table.cpp
- seed_table.h
- seqindex.cpp
- seqindex.h
- sequence.cpp
- sequence.h
- translate.h
- dispatch.h
- transpose.h
- transpose16x16.h
- transpose32x32.h
- vector.h
- vector8_avx2.h
- vector8_avx512.h
- vector8_neon.h
- vector8_sse.h
- vector_generic.h
- string.cpp
- string.h
- tokenizer.h
- endianness.h
- getRSS.cpp
- system.cpp
- system.h
- binary_buffer.h
- command_line_parser.cpp
- command_line_parser.h
- enum.h
- escape_sequences.h
- hash_function.h
- heartbeat.h
- intrin.h
- log_stream.h
- optional.h
- ptr_vector.h
- range.h
- simd.cpp
- simd.h
- system.h
- table.h
- text_buffer.h
- util.cpp
- util.h
- ChangeLog
- compile-osx.sh
- .cirrus.yml
- .dockerignore
- .gitattributes
- .gitignore
- CITATION.cff
- CMakeLists.txt
- Dockerfile
- LICENSE
- README.md
- TRADEMARKS
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/bbuchfink/diamond
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd diamond
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. Docker
쉬움 추천사전 준비물
- Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
- Docker Desktop 컨테이너를 빌드하고 실행하려면 필요합니다. 설치 후 실행해서 백그라운드에 켜두세요.
docker build -t diamond .
Dockerfile을 기반으로 실행 가능한 이미지를 빌드합니다.
docker run -p 8080:80 diamond
빌드된 이미지를 실제 컨테이너로 실행합니다.
터미널에 docker compose ps 를 입력해 컨테이너들이 Up 상태인지 확인하세요. README에 포트 번호가 적혀있다면 브라우저에서 http://localhost:포트번호 로 접속해보세요.
3. CMake
보통사전 준비물
mkdir build && cd build
빌드 결과물을 담을 폴더를 만들고 그 안으로 이동합니다.
cmake ..
소스코드를 분석해 빌드 설정 파일을 생성합니다 (build 폴더 안에서 실행해야 함).
make
생성된 빌드 설정을 바탕으로 실제 컴파일을 진행해 실행 파일을 만듭니다.
build 폴더 안에 실행 파일이 생성됐는지 확인하고, 직접 실행해보세요 (예: ./build/앱이름).
// repository documentation
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