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[pkgsrc/trunk]: pkgsrc/biology/ncbi-blast+ biology/ncbi-blast+: Update to 2.11.0
details: https://anonhg.NetBSD.org/pkgsrc/rev/3050c8364a8c
branches: trunk
changeset: 454426:3050c8364a8c
user: bacon <bacon%pkgsrc.org@localhost>
date: Fri Jun 11 13:47:39 2021 +0000
description:
biology/ncbi-blast+: Update to 2.11.0
Release notes: https://www.ncbi.nlm.nih.gov/books/NBK131777/
diffstat:
biology/ncbi-blast+/Makefile | 10 +-
biology/ncbi-blast+/PLIST | 141 +++++++++-
biology/ncbi-blast+/buildlink3.mk | 4 +-
biology/ncbi-blast+/distinfo | 15 +-
biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh | 15 -
biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh | 15 +
biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure | 15 -
biology/ncbi-blast+/patches/patch-src_build-system_configure | 10 +-
8 files changed, 171 insertions(+), 54 deletions(-)
diffs (truncated from 595 to 300 lines):
diff -r 823eaa73497f -r 3050c8364a8c biology/ncbi-blast+/Makefile
--- a/biology/ncbi-blast+/Makefile Fri Jun 11 10:37:27 2021 +0000
+++ b/biology/ncbi-blast+/Makefile Fri Jun 11 13:47:39 2021 +0000
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.23 2021/05/24 19:49:11 wiz Exp $
+# $NetBSD: Makefile,v 1.24 2021/06/11 13:47:39 bacon Exp $
-DISTNAME= ncbi-blast-2.8.1+-src
+DISTNAME= ncbi-blast-2.11.0+-src
PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/}
-PKGREVISION= 15
CATEGORIES= biology
MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
@@ -19,7 +18,7 @@
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
+SUBST_FILES.configure+= src/build-system/configure
USE_TOOLS+= bash gmake perl
USE_LANGUAGES= c c++
@@ -29,6 +28,7 @@
REPLACE_BASH+= src/app/blast/get_species_taxids.sh
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
+REPLACE_PYTHON+= src/app/blast/cleanup-blastdb-volumes.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
@@ -54,7 +54,9 @@
post-install:
${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
+.if ${OPSYS} != Darwin
${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so
+.endif
.include "../../devel/zlib/buildlink3.mk"
.include "../../archivers/lzo/buildlink3.mk"
diff -r 823eaa73497f -r 3050c8364a8c biology/ncbi-blast+/PLIST
--- a/biology/ncbi-blast+/PLIST Fri Jun 11 10:37:27 2021 +0000
+++ b/biology/ncbi-blast+/PLIST Fri Jun 11 13:47:39 2021 +0000
@@ -1,13 +1,16 @@
-@comment $NetBSD: PLIST,v 1.2 2019/01/07 15:00:10 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/06/11 13:47:39 bacon Exp $
bin/blast_formatter
+bin/blast_report
bin/blastdb_aliastool
bin/blastdb_convert
+bin/blastdb_path
bin/blastdbcheck
bin/blastdbcmd
bin/blastdbcp
bin/blastn
bin/blastp
bin/blastx
+bin/cleanup-blastdb-volumes.py
bin/convert2blastmask
bin/datatool
bin/deltablast
@@ -40,6 +43,7 @@
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_node.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
@@ -50,6 +54,7 @@
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/blast_usage_report.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
@@ -273,6 +278,8 @@
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_revision.h
+include/ncbi-tools++/common/ncbi_revision.h.in
include/ncbi-tools++/common/ncbi_skew_guard.h
include/ncbi-tools++/common/ncbi_source_ver.cmake_nodep
include/ncbi-tools++/common/ncbi_source_ver.h
@@ -286,6 +293,7 @@
include/ncbi-tools++/connect/impl/server_connection.hpp
include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp
include/ncbi-tools++/connect/ncbi_base64.h
+include/ncbi-tools++/connect/ncbi_blowfish.h
include/ncbi-tools++/connect/ncbi_buffer.h
include/ncbi-tools++/connect/ncbi_conn_exception.hpp
include/ncbi-tools++/connect/ncbi_conn_reader_writer.hpp
@@ -307,6 +315,7 @@
include/ncbi-tools++/connect/ncbi_ipv6.h
include/ncbi-tools++/connect/ncbi_lbos.hpp
include/ncbi-tools++/connect/ncbi_localip.h
+include/ncbi-tools++/connect/ncbi_localip.hpp
include/ncbi-tools++/connect/ncbi_mbedtls.h
include/ncbi-tools++/connect/ncbi_memory_connector.h
include/ncbi-tools++/connect/ncbi_misc.hpp
@@ -318,6 +327,7 @@
include/ncbi-tools++/connect/ncbi_sendmail.h
include/ncbi-tools++/connect/ncbi_server_info.h
include/ncbi-tools++/connect/ncbi_service.h
+include/ncbi-tools++/connect/ncbi_service.hpp
include/ncbi-tools++/connect/ncbi_service_connector.h
include/ncbi-tools++/connect/ncbi_service_cxx.hpp
include/ncbi-tools++/connect/ncbi_socket.h
@@ -327,6 +337,7 @@
include/ncbi-tools++/connect/ncbi_socket_unix.hpp
include/ncbi-tools++/connect/ncbi_tls.h
include/ncbi-tools++/connect/ncbi_types.h
+include/ncbi-tools++/connect/ncbi_usage_report.hpp
include/ncbi-tools++/connect/ncbi_userhost.hpp
include/ncbi-tools++/connect/ncbi_util.h
include/ncbi-tools++/connect/server.hpp
@@ -427,6 +438,7 @@
include/ncbi-tools++/corelib/ncbi_url.hpp
include/ncbi-tools++/corelib/ncbi_xstr.hpp
include/ncbi-tools++/corelib/ncbiapp.hpp
+include/ncbi-tools++/corelib/ncbiapp_api.hpp
include/ncbi-tools++/corelib/ncbiargs.hpp
include/ncbi-tools++/corelib/ncbiatomic.h
include/ncbi-tools++/corelib/ncbiatomic.hpp
@@ -454,6 +466,7 @@
include/ncbi-tools++/corelib/ncbistr.hpp
include/ncbi-tools++/corelib/ncbistr_util.hpp
include/ncbi-tools++/corelib/ncbistre.hpp
+include/ncbi-tools++/corelib/ncbisys.hpp
include/ncbi-tools++/corelib/ncbithr.hpp
include/ncbi-tools++/corelib/ncbithr_conf.hpp
include/ncbi-tools++/corelib/ncbitime.hpp
@@ -478,6 +491,7 @@
include/ncbi-tools++/corelib/test_boost.hpp
include/ncbi-tools++/corelib/test_mt.hpp
include/ncbi-tools++/corelib/version.hpp
+include/ncbi-tools++/corelib/version_api.hpp
include/ncbi-tools++/db/error_codes.hpp
include/ncbi-tools++/db/sqlite/sqlitewrapp.hpp
include/ncbi-tools++/dbapi/cache/dbapi_blob_cache.hpp
@@ -497,6 +511,7 @@
include/ncbi-tools++/dbapi/driver/impl/dbapi_impl_connection.hpp
include/ncbi-tools++/dbapi/driver/impl/dbapi_impl_context.hpp
include/ncbi-tools++/dbapi/driver/impl/dbapi_impl_result.hpp
+include/ncbi-tools++/dbapi/driver/impl/dbapi_pool_balancer.hpp
include/ncbi-tools++/dbapi/driver/impl/handle_stack.hpp
include/ncbi-tools++/dbapi/driver/interfaces.hpp
include/ncbi-tools++/dbapi/driver/odbc/interfaces.hpp
@@ -535,6 +550,76 @@
include/ncbi-tools++/html/selection.hpp
include/ncbi-tools++/html/writer_htmlenc.hpp
include/ncbi-tools++/misc/error_codes.hpp
+include/ncbi-tools++/misc/jsonwrapp/jsonwrapp.hpp
+include/ncbi-tools++/misc/jsonwrapp/jsonwrapp10.hpp
+include/ncbi-tools++/misc/jsonwrapp/jsonwrapp11.hpp
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/__NCBI_read_me.txt
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/allocators.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/document.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/encodedstream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/encodings.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/error/en.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/error/error.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/filereadstream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/filewritestream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/biginteger.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/diyfp.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/dtoa.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/ieee754.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/itoa.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/meta.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/pow10.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/stack.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/strfunc.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/strtod.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/license.txt
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/memorybuffer.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/memorystream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/msinttypes/inttypes.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/msinttypes/stdint.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/pointer.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/prettywriter.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/rapidjson.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/reader.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/stringbuffer.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson10/writer.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/__NCBI_read_me.txt
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/allocators.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/document.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/encodedstream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/encodings.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/error/en.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/error/error.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/filereadstream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/filewritestream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/fwd.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/biginteger.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/diyfp.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/dtoa.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/ieee754.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/itoa.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/meta.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/pow10.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/regex.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/stack.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/strfunc.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/strtod.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/swap.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/istreamwrapper.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/license.txt
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/memorybuffer.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/memorystream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/msinttypes/inttypes.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/msinttypes/stdint.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/ostreamwrapper.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/pointer.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/prettywriter.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/rapidjson.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/reader.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/schema.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/stream.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/stringbuffer.h
+include/ncbi-tools++/misc/jsonwrapp/rapidjson11/writer.h
include/ncbi-tools++/ncbi_pch.hpp
include/ncbi-tools++/ncbi_random_macro.h
include/ncbi-tools++/ncbi_source_ver.h
@@ -946,6 +1031,10 @@
include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set_.hpp
include/ncbi-tools++/objects/coords/NCBI_HGVSCoordinate_module.hpp
include/ncbi-tools++/objects/coords/objcoords__.hpp
+include/ncbi-tools++/objects/dbsnp/primary_track/dbsnp.grpc.pb.h
+include/ncbi-tools++/objects/dbsnp/primary_track/dbsnp.pb.h
+include/ncbi-tools++/objects/dbsnp/primary_track/impl/snpptis_impl.hpp
+include/ncbi-tools++/objects/dbsnp/primary_track/snpptis.hpp
include/ncbi-tools++/objects/docsum/.cvsignore
include/ncbi-tools++/objects/docsum/.gitignore
include/ncbi-tools++/objects/docsum/Assay.hpp
@@ -1219,6 +1308,8 @@
include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse_.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_SequenceInfo.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_SequenceInfo_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLx.hpp
@@ -3398,6 +3489,7 @@
include/ncbi-tools++/objtools/alnmgr/aln_converters.hpp
include/ncbi-tools++/objtools/alnmgr/aln_explorer.hpp
include/ncbi-tools++/objtools/alnmgr/aln_generators.hpp
+include/ncbi-tools++/objtools/alnmgr/aln_rng_coll_list_oper.hpp
include/ncbi-tools++/objtools/alnmgr/aln_rng_coll_oper.hpp
include/ncbi-tools++/objtools/alnmgr/aln_seqid.hpp
include/ncbi-tools++/objtools/alnmgr/aln_serial.hpp
@@ -3464,7 +3556,9 @@
include/ncbi-tools++/objtools/cleanup/capitalization_string.hpp
include/ncbi-tools++/objtools/cleanup/cleanup.hpp
include/ncbi-tools++/objtools/cleanup/cleanup_change.hpp
-include/ncbi-tools++/objtools/cleanup/newcleanup.hpp
+include/ncbi-tools++/objtools/cleanup/cleanup_message.hpp
+include/ncbi-tools++/objtools/cleanup/cleanup_pub.hpp
+include/ncbi-tools++/objtools/cleanup/fix_feature_id.hpp
include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader.hpp
include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader_rmt.hpp
include/ncbi-tools++/objtools/data_loaders/blastdb/blastdb_adapter.hpp
@@ -3476,6 +3570,7 @@
include/ncbi-tools++/objtools/data_loaders/genbank/cache/writer_cache_entry.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gbloader.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gbloader_params.h
+include/ncbi-tools++/objtools/data_loaders/genbank/gbnative.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gicache/reader_gicache.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gicache/reader_gicache_entry.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gicache/reader_gicache_params.h
@@ -3492,12 +3587,14 @@
include/ncbi-tools++/objtools/data_loaders/genbank/impl/info_cache.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/processor.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/processors.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id1_base.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_service.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/request_result.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/standalone_result.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/statistics.hpp
+include/ncbi-tools++/objtools/data_loaders/genbank/psg_loader.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader_interface.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader_params.h
@@ -3514,7 +3611,6 @@
include/ncbi-tools++/objtools/data_loaders/genbank/writer.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/writer_interface.hpp
include/ncbi-tools++/objtools/data_loaders/loaders.hpp
-include/ncbi-tools++/objtools/edit/apply_mods.hpp
include/ncbi-tools++/objtools/edit/apply_object.hpp
include/ncbi-tools++/objtools/edit/autodef.hpp
include/ncbi-tools++/objtools/edit/autodef_options.hpp
@@ -3541,6 +3637,7 @@
include/ncbi-tools++/objtools/edit/publication_edit.hpp
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