git: b324d354c77d - main - biology/ncbi-blast+: Update to 2.16.0

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Tue, 14 Jan 2025 17:47:33 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=b324d354c77d38829dfde770cdd9799e69462442

commit b324d354c77d38829dfde770cdd9799e69462442
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-01-14 17:43:59 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-01-14 17:43:59 +0000

    biology/ncbi-blast+: Update to 2.16.0
    
    Several minor improvements and bug fixes
    Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/
    Minor clean up in port Makefile
    
    PR:             283250
    Reported by:    alster@vinterdalen.se
---
 biology/ncbi-blast+/Makefile  | 41 ++++++++++++++++++++---------------------
 biology/ncbi-blast+/distinfo  |  6 +++---
 biology/ncbi-blast+/pkg-plist | 14 +++++++++++---
 3 files changed, 34 insertions(+), 27 deletions(-)

diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index 8479e38ff8ea..e6ef9db191cc 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	ncbi-blast+
-DISTVERSION=	2.14.1
-PORTREVISION=	8
+DISTVERSION=	2.16.0
 CATEGORIES=	biology perl5 python
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
 		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
@@ -8,7 +7,7 @@ DISTNAME=	ncbi-blast-${PORTVERSION}+-src
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
-WWW=		https://blast.ncbi.nlm.nih.gov
+WWW=		https://blast.ncbi.nlm.nih.gov/
 
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
@@ -16,35 +15,35 @@ LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
 ONLY_FOR_ARCHS=		aarch64 amd64 powerpc64 powerpc64le riscv64
 ONLY_FOR_ARCHS_REASON=	Requires 64-bit processor
 
-LIB_DEPENDS=	libpcre.so:devel/pcre \
-		liblmdb.so:databases/lmdb \
-		liblzo2.so:archivers/lzo2 \
-		libgnutls.so:security/gnutls \
-		libtspi.so:security/trousers \
+LIB_DEPENDS=	libdw.so:devel/elfutils \
+		libgcrypt.so:security/libgcrypt \
 		libgmp.so:math/gmp \
+		libgnutls.so:security/gnutls \
+		libgpg-error.so:security/libgpg-error \
+		libgrpc.so:devel/grpc \
+		libhogweed.so:security/nettle \
 		libidn2.so:dns/libidn2 \
+		liblmdb.so:databases/lmdb \
+		liblzo2.so:archivers/lzo2 \
 		libnettle.so:security/nettle \
-		libhogweed.so:security/nettle \
-		libtasn1.so:security/libtasn1 \
+		libnghttp2.so:www/libnghttp2 \
 		libp11-kit.so:security/p11-kit \
-		libgcrypt.so:security/libgcrypt \
-		libgpg-error.so:security/libgpg-error \
+		libpcre.so:devel/pcre \
 		libsqlite3.so:databases/sqlite3 \
+		libtasn1.so:security/libtasn1 \
+		libtspi.so:security/trousers \
 		libuv.so:devel/libuv \
-		libnghttp2.so:www/libnghttp2 \
-		libgrpc.so:devel/grpc \
-		libzstd.so:archivers/zstd \
-		libdw.so:devel/elfutils
+		libzstd.so:archivers/zstd
 RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
 		p5-JSON>=0:converters/p5-JSON
 
-USES=		compiler:c++14-lang gmake localbase:ldflags shebangfix perl5 python
-USE_LDCONFIG=	yes
+USES=		compiler:c++14-lang gmake localbase:ldflags perl5 python shebangfix
+USE_LDCONFIG=	${PREFIX}/lib/ncbi-tools++
 
-SHEBANG_FILES=	src/app/blast/legacy_blast.pl \
-		src/app/blast/update_blastdb.pl \
-		src/app/blast/cleanup-blastdb-volumes.py \
+SHEBANG_FILES=	src/app/blast/cleanup-blastdb-volumes.py \
 		src/app/blast/get_species_taxids.sh \
+		src/app/blast/legacy_blast.pl \
+		src/app/blast/update_blastdb.pl \
 		src/app/winmasker/windowmasker_2.2.22_adapter.py
 GNU_CONFIGURE=	yes
 
diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo
index 4af49f2b46ea..fb3f8ad65194 100644
--- a/biology/ncbi-blast+/distinfo
+++ b/biology/ncbi-blast+/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1692973880
-SHA256 (ncbi-blast-2.14.1+-src.tar.gz) = 712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e
-SIZE (ncbi-blast-2.14.1+-src.tar.gz) = 28258487
+TIMESTAMP = 1733904135
+SHA256 (ncbi-blast-2.16.0+-src.tar.gz) = 17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b
+SIZE (ncbi-blast-2.16.0+-src.tar.gz) = 28307712
diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
index a48efb2375e8..88452e690ca1 100644
--- a/biology/ncbi-blast+/pkg-plist
+++ b/biology/ncbi-blast+/pkg-plist
@@ -1,5 +1,4 @@
 bin/blast_formatter
-bin/blast_report
 bin/blastdb_aliastool
 bin/blastdb_convert
 bin/blastdb_path
@@ -31,6 +30,7 @@ bin/run_with_lock
 bin/seedtop
 bin/segmasker
 bin/seqdb_demo
+bin/tax4blast
 bin/tblastn
 bin/tblastx
 bin/update_blastdb.pl
@@ -255,6 +255,8 @@ 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/caf_encoded.hpp
+include/ncbi-tools++/cgi/caf_plain.hpp
 include/ncbi-tools++/cgi/cgi_exception.hpp
 include/ncbi-tools++/cgi/cgi_serial.hpp
 include/ncbi-tools++/cgi/cgi_session.hpp
@@ -277,6 +279,7 @@ 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_info.h
+include/ncbi-tools++/common/ncbi_build_ver.cmake_nodep
 include/ncbi-tools++/common/ncbi_build_ver.h
 include/ncbi-tools++/common/ncbi_build_ver.h.last
 include/ncbi-tools++/common/ncbi_export.h
@@ -1162,6 +1165,8 @@ include/ncbi-tools++/objects/gbproj/FolderInfo.hpp
 include/ncbi-tools++/objects/gbproj/FolderInfo_.hpp
 include/ncbi-tools++/objects/gbproj/GBProject_ver2.hpp
 include/ncbi-tools++/objects/gbproj/GBProject_ver2_.hpp
+include/ncbi-tools++/objects/gbproj/HugeFileProjectItem.hpp
+include/ncbi-tools++/objects/gbproj/HugeFileProjectItem_.hpp
 include/ncbi-tools++/objects/gbproj/LoaderDescriptor.hpp
 include/ncbi-tools++/objects/gbproj/LoaderDescriptor_.hpp
 include/ncbi-tools++/objects/gbproj/NCBI_GBProject_module.hpp
@@ -3490,11 +3495,13 @@ include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbisam.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbtax.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbvol.hpp
+include/ncbi-tools++/objtools/blast/seqdb_reader/itax4blast.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqdb.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbblob.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbcommon.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbexpert.hpp
 include/ncbi-tools++/objtools/blast/seqdb_reader/seqidlist_reader.hpp
+include/ncbi-tools++/objtools/blast/seqdb_reader/tax4blastsqlite.hpp
 include/ncbi-tools++/objtools/blast/seqdb_writer/build_db.hpp
 include/ncbi-tools++/objtools/blast/seqdb_writer/impl/criteria.hpp
 include/ncbi-tools++/objtools/blast/seqdb_writer/multisource_util.hpp
@@ -3514,7 +3521,7 @@ include/ncbi-tools++/objtools/cleanup/cleanup_change.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/cleanup/huge_file_cleanup.hpp
+include/ncbi-tools++/objtools/cleanup/influenza_set.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
@@ -3588,7 +3595,6 @@ include/ncbi-tools++/objtools/edit/gaps_edit.hpp
 include/ncbi-tools++/objtools/edit/gb_block_field.hpp
 include/ncbi-tools++/objtools/edit/gene_utils.hpp
 include/ncbi-tools++/objtools/edit/huge_asn_loader.hpp
-include/ncbi-tools++/objtools/edit/huge_asn_macro_reader.hpp
 include/ncbi-tools++/objtools/edit/huge_asn_reader.hpp
 include/ncbi-tools++/objtools/edit/huge_file.hpp
 include/ncbi-tools++/objtools/edit/huge_file_process.hpp
@@ -4445,6 +4451,7 @@ include/ncbi-tools++/objtools/format/feature_gather.hpp
 include/ncbi-tools++/objtools/format/flat_expt.hpp
 include/ncbi-tools++/objtools/format/flat_file_config.hpp
 include/ncbi-tools++/objtools/format/flat_file_generator.hpp
+include/ncbi-tools++/objtools/format/flat_file_html.hpp
 include/ncbi-tools++/objtools/format/format_item_ostream.hpp
 include/ncbi-tools++/objtools/format/formatter.hpp
 include/ncbi-tools++/objtools/format/ftable_formatter.hpp
@@ -4690,6 +4697,7 @@ include/ncbi-tools++/sra/readers/sra/limited_resource_map.hpp
 include/ncbi-tools++/sra/readers/sra/sdk.hpp
 include/ncbi-tools++/sra/readers/sra/snpread.hpp
 include/ncbi-tools++/sra/readers/sra/sraread.hpp
+include/ncbi-tools++/sra/readers/sra/vdbcache.hpp
 include/ncbi-tools++/sra/readers/sra/vdbread.hpp
 include/ncbi-tools++/sra/readers/sra/wgsread.hpp
 include/ncbi-tools++/sra/readers/sra/wgsresolver.hpp