Date: Tue, 14 Jan 2025 17:47:33 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: b324d354c77d - main - biology/ncbi-blast+: Update to 2.16.0 Message-ID: <202501141747.50EHlXi0054133@gitrepo.freebsd.org>
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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
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