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ncbi-blast+: Import ncbi-blast+-2.7.1 as wip/ncbi-blast+
Module Name: pkgsrc-wip
Committed By: Jason W Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Tue Mar 27 10:37:40 2018 -0500
Changeset: 72408b65713a3164a3930d5b66d95a6e9883c572
Modified Files:
Makefile
Added Files:
ncbi-blast+/DESCR
ncbi-blast+/Makefile
ncbi-blast+/PLIST
ncbi-blast+/distinfo
ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
ncbi-blast+/patches/patch-src_build-system_configure
Log Message:
ncbi-blast+: Import ncbi-blast+-2.7.1 as wip/ncbi-blast+
Deprecates wip/ncbi-blast, but keep both pending full testing
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=72408b65713a3164a3930d5b66d95a6e9883c572
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
ncbi-blast+/DESCR | 5 +
ncbi-blast+/Makefile | 82 +
ncbi-blast+/PLIST | 4113 ++++++++++++++++++++
ncbi-blast+/distinfo | 11 +
.../patches/patch-compilers_xcode30__prj_configure | 14 +
.../patch-src_algo_blast_core_blast__kappa.c | 30 +
.../patches/patch-src_build-system_Makefile.in.top | 36 +
.../patch-src_build-system_cmake_cmake-configure | 14 +
.../patches/patch-src_build-system_configure | 14 +
10 files changed, 4320 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index a13f822a90..304f776019 100644
--- a/Makefile
+++ b/Makefile
@@ -2180,6 +2180,7 @@ SUBDIR+= nbfc
SUBDIR+= ncbi
SUBDIR+= ncbi-bin
SUBDIR+= ncbi-blast
+SUBDIR+= ncbi-blast+
SUBDIR+= ncbi-c++-lib
SUBDIR+= ncbi-lib
SUBDIR+= ncp
diff --git a/ncbi-blast+/DESCR b/ncbi-blast+/DESCR
new file mode 100644
index 0000000000..0d7c1d401b
--- /dev/null
+++ b/ncbi-blast+/DESCR
@@ -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 --git a/ncbi-blast+/Makefile b/ncbi-blast+/Makefile
new file mode 100644
index 0000000000..30ceddc7b3
--- /dev/null
+++ b/ncbi-blast+/Makefile
@@ -0,0 +1,82 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Mon Mar 26 08:34:17 CDT 2018 #
+###########################################################
+
+# LIB_DEPENDS=
+# libtspi.so:security/trousers \
+
+DISTNAME= ncbi-blast-${PORTVERSION}+-src
+PKGNAME= ncbi-blast+-${PORTVERSION}
+CATEGORIES= biology
+MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
+ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
+
+MAINTAINER= jwb%FreeBSD.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+= thread
+SUBST_STAGE.thread= post-patch
+SUBST_SED.thread+= -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|'
+SUBST_SED.thread+= -e '/--infodir=DIR/d'
+SUBST_SED.thread+= -e '/--mandir=DIR/d'
+SUBST_FILES.thread+= ${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
+
+WRKSRC= ${WRKDIR}/${DISTNAME}/c++
+
+# 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
+# FreeBSD boost port flagged by configure as untested version
+CONFIGURE_ENV= ncbi_cv_prog_amq_w=no
+CONFIGURE_ARGS+= AR="ar cr" --without-boost
+CONFIGURE_ARGS+= --libdir=${PREFIX}/lib/ncbi-tools++
+
+CFLAGS+= -fopenmp
+CXXFLAGS+= -fopenmp
+MAKE_JOBS_SAFE= no # Intermittent issues
+
+PORTVERSION= 2.7.1
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == NetBSD
+# statfs is deprecated on NetBSD, but still exists in libc
+# configure checks only for undefined reference, not for usability
+CONFIGURE_ENV+= ac_cv_func_statfs=no
+.endif
+
+# --libdir=${PREFIX}/lib/ncbi-tools++ doesn't respect DESTDIR, so do
+# a postinstall mv.
+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 --git a/ncbi-blast+/PLIST b/ncbi-blast+/PLIST
new file mode 100644
index 0000000000..c91ed40d92
--- /dev/null
+++ b/ncbi-blast+/PLIST
@@ -0,0 +1,4113 @@
+@comment $NetBSD$
+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
+include/ncbi-tools++/algo/winmask/seq_masker_istat_factory.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_istat_oascii.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_istat_obinary.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_ostat.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_ostat_ascii.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_ostat_bin.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_ostat_factory.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_ascii.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_bin.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_score.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_score_mean.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_score_mean_glob.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_score_min.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_uset_array.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_uset_hash.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_uset_simple.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_util.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_version.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_window.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_window_ambig.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_window_pattern.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_window_pattern_ambig.hpp
+include/ncbi-tools++/algo/winmask/win_mask_config.hpp
+include/ncbi-tools++/algo/winmask/win_mask_counts_converter.hpp
+include/ncbi-tools++/algo/winmask/win_mask_dup_table.hpp
+include/ncbi-tools++/algo/winmask/win_mask_gen_counts.hpp
+include/ncbi-tools++/algo/winmask/win_mask_util.hpp
+include/ncbi-tools++/cgi/caf.hpp
+include/ncbi-tools++/cgi/cgi_exception.hpp
+include/ncbi-tools++/cgi/cgi_serial.hpp
+include/ncbi-tools++/cgi/cgi_session.hpp
+include/ncbi-tools++/cgi/cgi_util.hpp
+include/ncbi-tools++/cgi/cgiapp.hpp
+include/ncbi-tools++/cgi/cgiapp_cached.hpp
+include/ncbi-tools++/cgi/cgictx.hpp
+include/ncbi-tools++/cgi/error_codes.hpp
+include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp
+include/ncbi-tools++/cgi/ncbicgi.hpp
+include/ncbi-tools++/cgi/ncbicgir.hpp
+include/ncbi-tools++/cgi/ncbires.hpp
+include/ncbi-tools++/cgi/ref_args.hpp
+include/ncbi-tools++/cgi/user_agent.hpp
+include/ncbi-tools++/common/boost_skew_guard.hpp
+include/ncbi-tools++/common/config/ncbiconf_msvc.h
+include/ncbi-tools++/common/config/ncbiconf_universal.h
+include/ncbi-tools++/common/config/ncbiconf_xcode.h
+include/ncbi-tools++/common/header_template.hpp
+include/ncbi-tools++/common/metamodules_doxygen.h
+include/ncbi-tools++/common/ncbi_build_ver.h
+include/ncbi-tools++/common/ncbi_build_ver.h.in
+include/ncbi-tools++/common/ncbi_build_ver.h.last
+include/ncbi-tools++/common/ncbi_export.h
+include/ncbi-tools++/common/ncbi_package_ver.h
+include/ncbi-tools++/common/ncbi_pch_impl.hpp
+include/ncbi-tools++/common/ncbi_skew_guard.h
+include/ncbi-tools++/common/ncbi_source_ver.h
+include/ncbi-tools++/common/ncbiconf_impl.h
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+lib/ncbi-tools++/libxformat-static.a
+lib/ncbi-tools++/libxformat.a
+lib/ncbi-tools++/libxhtml-static.a
+lib/ncbi-tools++/libxhtml.a
+lib/ncbi-tools++/libxncbi-static.a
+lib/ncbi-tools++/libxncbi.a
+lib/ncbi-tools++/libxnetblast-static.a
+lib/ncbi-tools++/libxnetblast.a
+lib/ncbi-tools++/libxnetblastcli-static.a
+lib/ncbi-tools++/libxnetblastcli.a
+lib/ncbi-tools++/libxobjedit-static.a
+lib/ncbi-tools++/libxobjedit.a
+lib/ncbi-tools++/libxobjmgr-static.a
+lib/ncbi-tools++/libxobjmgr.a
+lib/ncbi-tools++/libxobjread-static.a
+lib/ncbi-tools++/libxobjread.a
+lib/ncbi-tools++/libxobjreadex-static.a
+lib/ncbi-tools++/libxobjreadex.a
+lib/ncbi-tools++/libxobjsimple-static.a
+lib/ncbi-tools++/libxobjsimple.a
+lib/ncbi-tools++/libxobjutil-static.a
+lib/ncbi-tools++/libxobjutil.a
+lib/ncbi-tools++/libxregexp-static.a
+lib/ncbi-tools++/libxregexp.a
+lib/ncbi-tools++/libxregexp_template_tester-static.a
+lib/ncbi-tools++/libxregexp_template_tester.a
+lib/ncbi-tools++/libxser-static.a
+lib/ncbi-tools++/libxser.a
+lib/ncbi-tools++/libxthrserv-static.a
+lib/ncbi-tools++/libxthrserv.a
+lib/ncbi-tools++/libxutil-static.a
+lib/ncbi-tools++/libxutil.a
+lib/ncbi-tools++/libxxconnect-static.a
+lib/ncbi-tools++/libxxconnect.a
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
new file mode 100644
index 0000000000..02f06d077b
--- /dev/null
+++ b/ncbi-blast+/distinfo
@@ -0,0 +1,11 @@
+$NetBSD$
+
+SHA1 (ncbi-blast-2.7.1+-src.tar.gz) = d04a25f01c386abd8515957a2ce1dabf376743f8
+RMD160 (ncbi-blast-2.7.1+-src.tar.gz) = 7277419e16fb215aae4136a16e13bec963b70cbd
+SHA512 (ncbi-blast-2.7.1+-src.tar.gz) = e4b3914f51165ae4c82051068ed9d3470687a4e0f1df6274018c0ba14b241666a570d72265c7d167b8ce2a9075652744244a00e3e95c00c4252da0fbd80d17c6
+Size (ncbi-blast-2.7.1+-src.tar.gz) = 23254824 bytes
+SHA1 (patch-compilers_xcode30__prj_configure) = d6bf60c1a12ef1ddd93af1bce87543a1d5156bea
+SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 0d0492bbb93d9ac48a9456bb5762c923ae84ffb9
+SHA1 (patch-src_build-system_Makefile.in.top) = 6e263f9eb1ba2a1b00a76ca0201e608531826d7b
+SHA1 (patch-src_build-system_cmake_cmake-configure) = e120568c934342c8003f89470d78b28f87ae48c4
+SHA1 (patch-src_build-system_configure) = cd2cffb73da34806c189f871799960f78a1a5a4d
diff --git a/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
new file mode 100644
index 0000000000..e04dbbad6c
--- /dev/null
+++ b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Fix portibility
+--- compilers/xcode30_prj/configure.orig 2018-03-26 14:12:13.368983690 +0000
++++ compilers/xcode30_prj/configure
+@@ -1,2 +1,2 @@
+-#!/bin/sh
++/bin/bash: indent: command not found
+
+@@ -282,3 +282,3 @@ platform=`xcodebuild -version 2>/dev/nul
+ # ------- target architecture
+-if test "$use_64" == "yes"; then
++if test "$use_64" = "yes"; then
+ use_arch="x86_64"
diff --git a/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c b/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
new file mode 100644
index 0000000000..939e2f7b16
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
@@ -0,0 +1,30 @@
+$NetBSD$
+
+# Work around NetBSD stderr def choking macro
+--- src/algo/blast/core/blast_kappa.c.orig 2018-03-26 21:55:44.000000000 +0000
++++ src/algo/blast/core/blast_kappa.c
+@@ -32,6 +32,7 @@
+ * system for each match in blastpgp
+ */
+
++#include <stdio.h>
+ #include <float.h>
+ #include <algo/blast/core/ncbi_math.h>
+ #include <algo/blast/core/blast_hits.h>
+@@ -3404,13 +3405,15 @@ Blast_RedoAlignmentCore_MT(EBlastProgram
+ }
+
+ Boolean interrupt = FALSE;
++ /* NetBSD defines stderr as (&__sF[2]), which the macro below chokes on */
++ FILE *my_stderr = stderr;
+ #pragma omp parallel \
+ default(none) num_threads(actual_num_threads) \
+ if(actual_num_threads>1) \
+ shared(interrupt, seqsrc_tld, score_params_tld, hit_params_tld, \
+ gap_align_tld, results_tld, \
+ redoneMatches_tld, \
+- stderr, \
++ my_stderr, \
+ numQueries, numMatches, theseMatches, \
+ numFrames, program_number, subjectBlk_tld, positionBased, \
+ default_db_genetic_code, localScalingFactor, queryInfo, \
diff --git a/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top b/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
new file mode 100644
index 0000000000..54f8202361
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
@@ -0,0 +1,36 @@
+$NetBSD$
+
+# Add destdir support
+
+--- src/build-system/Makefile.in.top.orig 2018-03-27 13:10:52.497034627 +0000
++++ src/build-system/Makefile.in.top
+@@ -37,21 +37,21 @@ check: $(PROJECTS)
+ fi
+
+ install-toolkit:
+- -$(RMDIR) $(pincludedir)
+- $(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
+- $(INSTALL) $(lbindir)/* $(bindir)
+- $(INSTALL) -m 644 $(llibdir)/*.* $(libdir)
++ -$(RMDIR) $(DESTDIR)$(pincludedir)
++ $(INSTALL) -d $(DESTDIR)$(bindir) $(DESTDIR)$(libdir) $(DESTDIR)$(pincludedir)
++ $(INSTALL) $(lbindir)/* $(DESTDIR)$(bindir)
++ $(INSTALL) -m 644 $(llibdir)/*.* $(DESTDIR)$(libdir)
+ if test -d $(llibdir)/ncbi; then \
+- cp -pPR $(llibdir)/ncbi $(libdir)/; \
++ cp -pPR $(llibdir)/ncbi $(DESTDIR)$(libdir)/; \
+ fi
+- -rm -f $(libdir)/lib*-static.a
+- cd $(libdir) && \
++ -rm -f $(DESTDIR)$(libdir)/lib*-static.a
++ cd $(DESTDIR)$(libdir) && \
+ for x in *.a; do \
+ $(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \
+ done
+ for d in $(includedir0) $(incdir); do \
+ cd $$d && find * -name .svn -prune -o -print | \
+- cpio -pd $(pincludedir) ; \
++ cpio -pd $(DESTDIR)$(pincludedir) ; \
+ done
+ ## set up appropriate build and status directories somewhere under $(libdir)?
+
diff --git a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
new file mode 100644
index 0000000000..a2b48f44b9
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Fix portability issue
+--- src/build-system/cmake/cmake-configure.orig 2018-03-26 14:13:44.229849356 +0000
++++ src/build-system/cmake/cmake-configure
+@@ -468,7 +468,7 @@ fi
+ if [ -z "$ROOT" ]; then
+ if [ -z "$GPIPEROOT" ]; then
+ ROOT="CMake-$BUILD_TYPE"
+- if [ "$BUILD_SHARED_LIBS" == "ON" ]; then
++ if [ "$BUILD_SHARED_LIBS" = "ON" ]; then
+ ROOT="$ROOT"DLL
+ fi
+ else
diff --git a/ncbi-blast+/patches/patch-src_build-system_configure b/ncbi-blast+/patches/patch-src_build-system_configure
new file mode 100644
index 0000000000..366e19784a
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_configure
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Fix support for localstatedir
+--- src/build-system/configure.orig 2018-02-19 01:32:40 UTC
++++ src/build-system/configure
+@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do
+ | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
+ | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
+ | --datadir=* | --sysconfdir=* | --localstatedir=* \
+- | --with-runpath=* | --with-relative-runpath=* \
++ | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
+ | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
+ | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
+ | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
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