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[pkgsrc/trunk]: pkgsrc/biology/ncbi-blast+ biology/ncbi-blast+: import ncbi-b...
details: https://anonhg.NetBSD.org/pkgsrc/rev/3ac2b7e1c860
branches: trunk
changeset: 379282:3ac2b7e1c860
user: bacon <bacon%pkgsrc.org@localhost>
date: Fri Apr 27 20:28:28 2018 +0000
description:
biology/ncbi-blast+: import ncbi-blast+-2.7.1
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity
between sequences. The program compares nucleotide or protein sequences to
sequence databases and calculates the statistical significance of matches.
BLAST can be used to infer functional and evolutionary relationships between
sequences as well as help identify members of gene families.
OK wiz@
diffstat:
biology/ncbi-blast+/DESCR | 5 +
biology/ncbi-blast+/Makefile | 68 +
biology/ncbi-blast+/PLIST | 4113 ++++++++++
biology/ncbi-blast+/buildlink3.mk | 13 +
biology/ncbi-blast+/distinfo | 12 +
biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure | 15 +
biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c | 31 +
biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top | 41 +
biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure | 15 +
biology/ncbi-blast+/patches/patch-src_build-system_configure | 15 +
biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app | 20 +
11 files changed, 4348 insertions(+), 0 deletions(-)
diffs (truncated from 4392 to 300 lines):
diff -r 9475630805ac -r 3ac2b7e1c860 biology/ncbi-blast+/DESCR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/ncbi-blast+/DESCR Fri Apr 27 20:28:28 2018 +0000
@@ -0,0 +1,5 @@
+The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity
+between sequences. The program compares nucleotide or protein sequences to
+sequence databases and calculates the statistical significance of matches.
+BLAST can be used to infer functional and evolutionary relationships between
+sequences as well as help identify members of gene families.
diff -r 9475630805ac -r 3ac2b7e1c860 biology/ncbi-blast+/Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/ncbi-blast+/Makefile Fri Apr 27 20:28:28 2018 +0000
@@ -0,0 +1,68 @@
+# $NetBSD: Makefile,v 1.1 2018/04/27 20:28:28 bacon Exp $
+
+DISTNAME= ncbi-blast-${PV}+-src
+PKGNAME= ncbi-blast+-${PV}
+CATEGORIES= biology
+MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
+ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= http://blast.ncbi.nlm.nih.gov/
+COMMENT= NCBI implementation of Basic Local Alignment Search Tool
+LICENSE= public-domain
+
+# Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0
+# Fix "unknown options" in configure
+SUBST_CLASSES+= configure
+SUBST_STAGE.configure= post-patch
+SUBST_SED.configure+= -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|'
+SUBST_SED.configure+= -e '/--infodir=DIR/d'
+SUBST_SED.configure+= -e '/--mandir=DIR/d'
+SUBST_FILES.configure+= ${WRKSRC}/src/build-system/configure
+
+USE_TOOLS+= gmake
+USE_LANGUAGES= c c++
+GNU_CONFIGURE= yes
+# REPLACE_BASH= compilers/xcode30_prj/configure
+REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
+REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py
+
+# The test for amq can hang, but amq is not needed so just avoid the test
+# configure chooses /usr/local/bin/ar with no flags
+# Resolve a conflict with libproj by moving libs to a subdir
+CONFIGURE_ENV= ncbi_cv_prog_amq_w=no
+CONFIGURE_ARGS+= AR="ar cr" --without-boost
+CONFIGURE_ARGS+= --libdir=${PREFIX}/lib/ncbi-tools++
+# MAKE_JOBS_SAFE= no # Intermittent issues
+WRKSRC= ${WRKDIR}/${DISTNAME}/c++
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == NetBSD
+# statfs is deprecated on NetBSD, but still exists in libc
+# configure checks only for undefined reference, not for usability
+CONFIGURE_ENV+= ac_cv_func_statfs=no
+.endif
+
+PV= 2.7.1
+
+post-install:
+ ${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
+ ${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/lzo/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../devel/pcre/buildlink3.mk"
+.include "../../databases/lmdb/buildlink3.mk"
+.include "../../security/gnutls/buildlink3.mk"
+.include "../../devel/gmp/buildlink3.mk"
+.include "../../devel/libidn2/buildlink3.mk"
+.include "../../security/nettle/buildlink3.mk"
+.include "../../security/libtasn1/buildlink3.mk"
+.include "../../security/p11-kit/buildlink3.mk"
+.include "../../security/libgcrypt/buildlink3.mk"
+.include "../../databases/sqlite3/buildlink3.mk"
+.include "../../security/libgpg-error/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff -r 9475630805ac -r 3ac2b7e1c860 biology/ncbi-blast+/PLIST
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/ncbi-blast+/PLIST Fri Apr 27 20:28:28 2018 +0000
@@ -0,0 +1,4113 @@
+@comment $NetBSD: PLIST,v 1.1 2018/04/27 20:28:28 bacon Exp $
+bin/blast_formatter
+bin/blastdb_aliastool
+bin/blastdbcheck
+bin/blastdbcmd
+bin/blastdbcp
+bin/blastn
+bin/blastp
+bin/blastx
+bin/convert2blastmask
+bin/datatool
+bin/deltablast
+bin/dustmasker
+bin/gc_cli
+bin/gene_info_reader
+bin/legacy_blast.pl
+bin/makeblastdb
+bin/makembindex
+bin/makeprofiledb
+bin/project_tree_builder
+bin/psiblast
+bin/rpsblast
+bin/rpstblastn
+bin/run_with_lock
+bin/seedtop
+bin/segmasker
+bin/seqdb_demo
+bin/seqdb_perf
+bin/tblastn
+bin/tblastx
+bin/update_blastdb.pl
+bin/windowmasker
+bin/windowmasker_2.2.22_adapter.py
+include/ncbi-tools++/algo/blast/api/bl2seq.hpp
+include/ncbi-tools++/algo/blast/api/blast_advprot_options.hpp
+include/ncbi-tools++/algo/blast/api/blast_aux.hpp
+include/ncbi-tools++/algo/blast/api/blast_dbindex.hpp
+include/ncbi-tools++/algo/blast/api/blast_exception.hpp
+include/ncbi-tools++/algo/blast/api/blast_mtlock.hpp
+include/ncbi-tools++/algo/blast/api/blast_nucl_options.hpp
+include/ncbi-tools++/algo/blast/api/blast_options.hpp
+include/ncbi-tools++/algo/blast/api/blast_options_builder.hpp
+include/ncbi-tools++/algo/blast/api/blast_options_handle.hpp
+include/ncbi-tools++/algo/blast/api/blast_prot_options.hpp
+include/ncbi-tools++/algo/blast/api/blast_results.hpp
+include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp
+include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp
+include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp
+include/ncbi-tools++/algo/blast/api/blast_types.hpp
+include/ncbi-tools++/algo/blast/api/blastp_kmer_options.hpp
+include/ncbi-tools++/algo/blast/api/blastx_options.hpp
+include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
+include/ncbi-tools++/algo/blast/api/deltablast.hpp
+include/ncbi-tools++/algo/blast/api/deltablast_options.hpp
+include/ncbi-tools++/algo/blast/api/disc_nucl_options.hpp
+include/ncbi-tools++/algo/blast/api/effsearchspace_calc.hpp
+include/ncbi-tools++/algo/blast/api/hspstream_queue.hpp
+include/ncbi-tools++/algo/blast/api/local_blast.hpp
+include/ncbi-tools++/algo/blast/api/local_db_adapter.hpp
+include/ncbi-tools++/algo/blast/api/local_search.hpp
+include/ncbi-tools++/algo/blast/api/magicblast.hpp
+include/ncbi-tools++/algo/blast/api/magicblast_options.hpp
+include/ncbi-tools++/algo/blast/api/msa_pssm_input.hpp
+include/ncbi-tools++/algo/blast/api/objmgr_query_data.hpp
+include/ncbi-tools++/algo/blast/api/objmgrfree_query_data.hpp
+include/ncbi-tools++/algo/blast/api/phiblast_nucl_options.hpp
+include/ncbi-tools++/algo/blast/api/phiblast_prot_options.hpp
+include/ncbi-tools++/algo/blast/api/prelim_stage.hpp
+include/ncbi-tools++/algo/blast/api/psi_pssm_input.hpp
+include/ncbi-tools++/algo/blast/api/psibl2seq.hpp
+include/ncbi-tools++/algo/blast/api/psiblast.hpp
+include/ncbi-tools++/algo/blast/api/psiblast_iteration.hpp
+include/ncbi-tools++/algo/blast/api/psiblast_options.hpp
+include/ncbi-tools++/algo/blast/api/pssm_engine.hpp
+include/ncbi-tools++/algo/blast/api/pssm_input.hpp
+include/ncbi-tools++/algo/blast/api/query_data.hpp
+include/ncbi-tools++/algo/blast/api/remote_blast.hpp
+include/ncbi-tools++/algo/blast/api/remote_search.hpp
+include/ncbi-tools++/algo/blast/api/repeats_filter.hpp
+include/ncbi-tools++/algo/blast/api/rps_aux.hpp
+include/ncbi-tools++/algo/blast/api/rpsblast_local.hpp
+include/ncbi-tools++/algo/blast/api/rpstblastn_options.hpp
+include/ncbi-tools++/algo/blast/api/search_strategy.hpp
+include/ncbi-tools++/algo/blast/api/seedtop.hpp
+include/ncbi-tools++/algo/blast/api/seqinfosrc_seqdb.hpp
+include/ncbi-tools++/algo/blast/api/seqinfosrc_seqvec.hpp
+include/ncbi-tools++/algo/blast/api/seqsrc_multiseq.hpp
+include/ncbi-tools++/algo/blast/api/seqsrc_seqdb.hpp
+include/ncbi-tools++/algo/blast/api/setup_factory.hpp
+include/ncbi-tools++/algo/blast/api/sseqloc.hpp
+include/ncbi-tools++/algo/blast/api/subj_ranges_set.hpp
+include/ncbi-tools++/algo/blast/api/tblastn_options.hpp
+include/ncbi-tools++/algo/blast/api/tblastx_options.hpp
+include/ncbi-tools++/algo/blast/api/traceback_stage.hpp
+include/ncbi-tools++/algo/blast/api/uniform_search.hpp
+include/ncbi-tools++/algo/blast/api/version.hpp
+include/ncbi-tools++/algo/blast/api/windowmask_filter.hpp
+include/ncbi-tools++/algo/blast/blastinput/blast_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/blast_asn1_input.hpp
+include/ncbi-tools++/algo/blast/blastinput/blast_fasta_input.hpp
+include/ncbi-tools++/algo/blast/blastinput/blast_input.hpp
+include/ncbi-tools++/algo/blast/blastinput/blast_input_aux.hpp
+include/ncbi-tools++/algo/blast/blastinput/blast_scope_src.hpp
+include/ncbi-tools++/algo/blast/blastinput/blastn_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/blastp_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/blastx_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
+include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/kblastp_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/rpsblast_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/rpstblastn_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/tblastn_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/tblastx_args.hpp
+include/ncbi-tools++/algo/blast/composition_adjustment/compo_heap.h
+include/ncbi-tools++/algo/blast/composition_adjustment/compo_mode_condition.h
+include/ncbi-tools++/algo/blast/composition_adjustment/composition_adjustment.h
+include/ncbi-tools++/algo/blast/composition_adjustment/composition_constants.h
+include/ncbi-tools++/algo/blast/composition_adjustment/matrix_frequency_data.h
+include/ncbi-tools++/algo/blast/composition_adjustment/nlm_linear_algebra.h
+include/ncbi-tools++/algo/blast/composition_adjustment/optimize_target_freq.h
+include/ncbi-tools++/algo/blast/composition_adjustment/redo_alignment.h
+include/ncbi-tools++/algo/blast/composition_adjustment/smith_waterman.h
+include/ncbi-tools++/algo/blast/composition_adjustment/unified_pvalues.h
+include/ncbi-tools++/algo/blast/core/aa_ungapped.h
+include/ncbi-tools++/algo/blast/core/blast_aalookup.h
+include/ncbi-tools++/algo/blast/core/blast_aascan.h
+include/ncbi-tools++/algo/blast/core/blast_def.h
+include/ncbi-tools++/algo/blast/core/blast_diagnostics.h
+include/ncbi-tools++/algo/blast/core/blast_encoding.h
+include/ncbi-tools++/algo/blast/core/blast_engine.h
+include/ncbi-tools++/algo/blast/core/blast_export.h
+include/ncbi-tools++/algo/blast/core/blast_extend.h
+include/ncbi-tools++/algo/blast/core/blast_filter.h
+include/ncbi-tools++/algo/blast/core/blast_gapalign.h
+include/ncbi-tools++/algo/blast/core/blast_hits.h
+include/ncbi-tools++/algo/blast/core/blast_hspfilter.h
+include/ncbi-tools++/algo/blast/core/blast_hspstream.h
+include/ncbi-tools++/algo/blast/core/blast_kappa.h
+include/ncbi-tools++/algo/blast/core/blast_lookup.h
+include/ncbi-tools++/algo/blast/core/blast_message.h
+include/ncbi-tools++/algo/blast/core/blast_nalookup.h
+include/ncbi-tools++/algo/blast/core/blast_nascan.h
+include/ncbi-tools++/algo/blast/core/blast_options.h
+include/ncbi-tools++/algo/blast/core/blast_parameters.h
+include/ncbi-tools++/algo/blast/core/blast_program.h
+include/ncbi-tools++/algo/blast/core/blast_psi.h
+include/ncbi-tools++/algo/blast/core/blast_query_info.h
+include/ncbi-tools++/algo/blast/core/blast_rps.h
+include/ncbi-tools++/algo/blast/core/blast_seg.h
+include/ncbi-tools++/algo/blast/core/blast_seqsrc.h
+include/ncbi-tools++/algo/blast/core/blast_seqsrc_impl.h
+include/ncbi-tools++/algo/blast/core/blast_setup.h
+include/ncbi-tools++/algo/blast/core/blast_stat.h
+include/ncbi-tools++/algo/blast/core/blast_sw.h
+include/ncbi-tools++/algo/blast/core/blast_toolkit.h
+include/ncbi-tools++/algo/blast/core/blast_traceback.h
+include/ncbi-tools++/algo/blast/core/blast_tune.h
+include/ncbi-tools++/algo/blast/core/blast_util.h
+include/ncbi-tools++/algo/blast/core/gapinfo.h
+include/ncbi-tools++/algo/blast/core/gencode_singleton.h
+include/ncbi-tools++/algo/blast/core/greedy_align.h
+include/ncbi-tools++/algo/blast/core/hspfilter_besthit.h
+include/ncbi-tools++/algo/blast/core/hspfilter_collector.h
+include/ncbi-tools++/algo/blast/core/hspfilter_culling.h
+include/ncbi-tools++/algo/blast/core/hspfilter_mapper.h
+include/ncbi-tools++/algo/blast/core/link_hsps.h
+include/ncbi-tools++/algo/blast/core/lookup_util.h
+include/ncbi-tools++/algo/blast/core/lookup_wrap.h
+include/ncbi-tools++/algo/blast/core/mb_indexed_lookup.h
+include/ncbi-tools++/algo/blast/core/na_ungapped.h
+include/ncbi-tools++/algo/blast/core/ncbi_math.h
+include/ncbi-tools++/algo/blast/core/ncbi_std.h
+include/ncbi-tools++/algo/blast/core/pattern.h
+include/ncbi-tools++/algo/blast/core/phi_extend.h
+include/ncbi-tools++/algo/blast/core/phi_gapalign.h
+include/ncbi-tools++/algo/blast/core/phi_lookup.h
+include/ncbi-tools++/algo/blast/core/spliced_hits.h
+include/ncbi-tools++/algo/blast/core/split_query.h
+include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp
+include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp
+include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp
+include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp
+include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp
+include/ncbi-tools++/algo/blast/format/blast_async_format.hpp
+include/ncbi-tools++/algo/blast/format/blast_format.hpp
+include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp
+include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp
+include/ncbi-tools++/algo/blast/format/blastxml_format.hpp
+include/ncbi-tools++/algo/blast/format/build_archive.hpp
+include/ncbi-tools++/algo/blast/format/data4xml2format.hpp
+include/ncbi-tools++/algo/blast/format/data4xmlformat.hpp
+include/ncbi-tools++/algo/blast/format/sam.hpp
+include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
+include/ncbi-tools++/algo/blast/igblast/igblast.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmer.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerindex.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmeroptions.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerresults.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerutils.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/kblastapi.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/mhfile.hpp
+include/ncbi-tools++/algo/dustmask/sdust.tex
+include/ncbi-tools++/algo/dustmask/symdust.hpp
+include/ncbi-tools++/algo/segmask/segmask.hpp
+include/ncbi-tools++/algo/winmask/README.API
+include/ncbi-tools++/algo/winmask/seq_masker.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_cache_boost.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_istat.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_istat_ascii.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_istat_bin.hpp
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