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[pkgsrc/trunk]: pkgsrc/biology/ncbi-blast+ ncbi-blast+: Upgrade to 2.8.1
details: https://anonhg.NetBSD.org/pkgsrc/rev/151eddc0daa3
branches: trunk
changeset: 327726:151eddc0daa3
user: bacon <bacon%pkgsrc.org@localhost>
date: Mon Jan 07 15:00:10 2019 +0000
description:
ncbi-blast+: Upgrade to 2.8.1
Support for new BLAST database format
Increased makeblastdb output file size limit to 4GB
Other minor bug fixes and enhancements
OK wiz@
diffstat:
biology/ncbi-blast+/Makefile | 17 +-
biology/ncbi-blast+/PLIST | 97 ++++++++-
biology/ncbi-blast+/distinfo | 14 +-
biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c | 23 +-
biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh | 15 +
biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h | 29 ++
6 files changed, 157 insertions(+), 38 deletions(-)
diffs (truncated from 528 to 300 lines):
diff -r ab4561947758 -r 151eddc0daa3 biology/ncbi-blast+/Makefile
--- a/biology/ncbi-blast+/Makefile Mon Jan 07 14:02:01 2019 +0000
+++ b/biology/ncbi-blast+/Makefile Mon Jan 07 15:00:10 2019 +0000
@@ -1,11 +1,10 @@
-# $NetBSD: Makefile,v 1.5 2018/12/09 18:52:17 adam Exp $
+# $NetBSD: Makefile,v 1.6 2019/01/07 15:00:10 bacon Exp $
-DISTNAME= ncbi-blast-${PV}+-src
-PKGNAME= ncbi-blast+-${PV}
-PKGREVISION= 3
+DISTNAME= ncbi-blast-2.8.1+-src
+PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/}
CATEGORIES= biology
MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
- https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/
+ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= http://blast.ncbi.nlm.nih.gov/
@@ -21,10 +20,11 @@
SUBST_SED.configure+= -e '/--mandir=DIR/d'
SUBST_FILES.configure+= ${WRKSRC}/src/build-system/configure
-USE_TOOLS+= gmake
+USE_TOOLS+= bash gmake
USE_LANGUAGES= c c++
GNU_CONFIGURE= yes
-# REPLACE_BASH= compilers/xcode30_prj/configure
+REPLACE_BASH= scripts/common/impl/define_random_macros.sh
+REPLACE_BASH+= src/app/blast/get_species_taxids.sh
REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py
@@ -34,7 +34,6 @@
CONFIGURE_ENV= ncbi_cv_prog_amq_w=no
CONFIGURE_ARGS+= AR="ar cr" --without-boost
CONFIGURE_ARGS+= --libdir=${PREFIX}/lib/ncbi-tools++
-# MAKE_JOBS_SAFE= no # Intermittent issues
WRKSRC= ${WRKDIR}/${DISTNAME}/c++
.include "../../mk/bsd.prefs.mk"
@@ -45,8 +44,6 @@
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
diff -r ab4561947758 -r 151eddc0daa3 biology/ncbi-blast+/PLIST
--- a/biology/ncbi-blast+/PLIST Mon Jan 07 14:02:01 2019 +0000
+++ b/biology/ncbi-blast+/PLIST Mon Jan 07 15:00:10 2019 +0000
@@ -1,6 +1,7 @@
-@comment $NetBSD: PLIST,v 1.1 2018/04/27 20:28:28 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2019/01/07 15:00:10 bacon Exp $
bin/blast_formatter
bin/blastdb_aliastool
+bin/blastdb_convert
bin/blastdbcheck
bin/blastdbcmd
bin/blastdbcp
@@ -13,7 +14,9 @@
bin/dustmasker
bin/gc_cli
bin/gene_info_reader
+bin/get_species_taxids.sh
bin/legacy_blast.pl
+bin/lmdbxx_sample
bin/makeblastdb
bin/makembindex
bin/makeprofiledb
@@ -258,10 +261,12 @@
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_msvc_site.h.in
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_info.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
@@ -269,6 +274,7 @@
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.cmake_nodep
include/ncbi-tools++/common/ncbi_source_ver.h
include/ncbi-tools++/common/ncbiconf_impl.h
include/ncbi-tools++/common/test_assert.h
@@ -313,6 +319,7 @@
include/ncbi-tools++/connect/ncbi_server_info.h
include/ncbi-tools++/connect/ncbi_service.h
include/ncbi-tools++/connect/ncbi_service_connector.h
+include/ncbi-tools++/connect/ncbi_service_cxx.hpp
include/ncbi-tools++/connect/ncbi_socket.h
include/ncbi-tools++/connect/ncbi_socket.hpp
include/ncbi-tools++/connect/ncbi_socket_connector.h
@@ -335,6 +342,7 @@
include/ncbi-tools++/connect/services/grid_rw_impl.hpp
include/ncbi-tools++/connect/services/grid_worker.hpp
include/ncbi-tools++/connect/services/grid_worker_app.hpp
+include/ncbi-tools++/connect/services/impl/netcache_api_int.hpp
include/ncbi-tools++/connect/services/impl/neticache_client_int.hpp
include/ncbi-tools++/connect/services/impl/netschedule_api_int.hpp
include/ncbi-tools++/connect/services/impl/netstorage_impl.hpp
@@ -400,6 +408,7 @@
include/ncbi-tools++/corelib/ncbi_bswap.hpp
include/ncbi-tools++/corelib/ncbi_config.hpp
include/ncbi-tools++/corelib/ncbi_cookies.hpp
+include/ncbi-tools++/corelib/ncbi_fast.hpp
include/ncbi-tools++/corelib/ncbi_limits.h
include/ncbi-tools++/corelib/ncbi_limits.hpp
include/ncbi-tools++/corelib/ncbi_mask.hpp
@@ -1200,28 +1209,20 @@
include/ncbi-tools++/objects/genomecoll/GCClient_AssemblyInfo_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_AssemblySequenceI.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_AssemblySequenceI_.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_AttributeFlags.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_AttributeFlags_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_EquivalentAssembl.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_EquivalentAssembl_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_Error.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_Error_.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyF.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyF_.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyR.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyR_.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyS.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyS_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBlobRe.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBlobRe_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ_.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyReques.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyReques_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse_.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
+include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLx_.hpp
include/ncbi-tools++/objects/genomecoll/GC_Assemblies.hpp
include/ncbi-tools++/objects/genomecoll/GC_Assemblies_.hpp
include/ncbi-tools++/objects/genomecoll/GC_Assembly.hpp
@@ -2923,6 +2924,7 @@
include/ncbi-tools++/objects/taxon1/Taxon1_resp_.hpp
include/ncbi-tools++/objects/taxon1/Taxon2_data.hpp
include/ncbi-tools++/objects/taxon1/Taxon2_data_.hpp
+include/ncbi-tools++/objects/taxon1/local_taxon.hpp
include/ncbi-tools++/objects/taxon1/taxon1.hpp
include/ncbi-tools++/objects/taxon1/taxon1__.hpp
include/ncbi-tools++/objects/taxon3/.cvsignore
@@ -2991,6 +2993,10 @@
include/ncbi-tools++/objects/trackmgr/TMgr_BlastRIDRequest_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_ClientInfo.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_ClientInfo_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRepl.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRepl_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRequ.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRequ_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetReply.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetReply_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetRequest.hpp
@@ -3001,6 +3007,8 @@
include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReply_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReques.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReques_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_DHubId.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_DHubId_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_DTrackId.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_DTrackId_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_DatasetItem.hpp
@@ -3017,6 +3025,10 @@
include/ncbi-tools++/objects/trackmgr/TMgr_DisplayTrack_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_GenomeContext.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_GenomeContext_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_Hub.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_HubTrack.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_HubTrack_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_Hub_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_Identity.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_IdentityId.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_IdentityIdType.hpp
@@ -3041,6 +3053,8 @@
include/ncbi-tools++/objects/trackmgr/TMgr_RemoveUserTrackReques_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectio.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectio_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectix.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectix_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_Reply.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_Reply_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_Request.hpp
@@ -3057,6 +3071,8 @@
include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRx.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRx_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextRep.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextRep_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextReq.hpp
@@ -3083,9 +3099,12 @@
include/ncbi-tools++/objects/trackmgr/TMgr_TrackSet_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_TypeStat.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_TypeStat_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_TypeTrackType.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_TypeTrackType_.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_ValueRequest.hpp
include/ncbi-tools++/objects/trackmgr/TMgr_ValueRequest_.hpp
include/ncbi-tools++/objects/trackmgr/blast_client.hpp
+include/ncbi-tools++/objects/trackmgr/createremotetrack_client.hpp
include/ncbi-tools++/objects/trackmgr/createtrackset_client.hpp
include/ncbi-tools++/objects/trackmgr/createusertrack_client.hpp
include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp
@@ -3141,6 +3160,30 @@
include/ncbi-tools++/objects/variation/VariationMethod_.hpp
include/ncbi-tools++/objects/variation/Variation_.hpp
include/ncbi-tools++/objects/variation/variation__.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/.cvsignore
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/.gitignore
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Error.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Error_.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/NCBI_search_by_rsid_module.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Placement.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Placement_.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/SearchByRsIdReply.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/SearchByRsIdReply_.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/search_by_rsid__.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/.cvsignore
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/.gitignore
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipData.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipData_.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSection.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSectionValue.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSectionValue_.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSection_.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceError.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceError_.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceReply.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceReply_.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/NCBI_dbsnp_tooltips_module.hpp
+include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/dbsnp_tooltip_service__.hpp
include/ncbi-tools++/objects/varrep/.cvsignore
include/ncbi-tools++/objects/varrep/.gitignore
include/ncbi-tools++/objects/varrep/AaInterval.hpp
@@ -3390,6 +3433,8 @@
include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp
include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info_reader.hpp
include/ncbi-tools++/objtools/blast/seqdb_reader/column_reader.hpp
+include/ncbi-tools++/objtools/blast/seqdb_reader/impl/lmdb++.h
+include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp
include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp
include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbcol.hpp
include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbfile.hpp
@@ -3401,9 +3446,11 @@
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_writer/build_db.hpp
include/ncbi-tools++/objtools/blast/seqdb_writer/impl/criteria.hpp
include/ncbi-tools++/objtools/blast/seqdb_writer/multisource_util.hpp
+include/ncbi-tools++/objtools/blast/seqdb_writer/seqidlist_writer.hpp
include/ncbi-tools++/objtools/blast/seqdb_writer/taxid_set.hpp
include/ncbi-tools++/objtools/blast/seqdb_writer/writedb.hpp
include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_convert.hpp
@@ -3411,8 +3458,10 @@
include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_files.hpp
include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_general.hpp
include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_isam.hpp
+include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_lmdb.hpp
include/ncbi-tools++/objtools/blast/services/blast_services.hpp
include/ncbi-tools++/objtools/cleanup/autogenerated_cleanup.hpp
+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
@@ -3465,6 +3514,7 @@
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
@@ -3473,8 +3523,11 @@
include/ncbi-tools++/objtools/edit/capitalization_string.hpp
include/ncbi-tools++/objtools/edit/cds_fix.hpp
include/ncbi-tools++/objtools/edit/dblink_field.hpp
+include/ncbi-tools++/objtools/edit/edit_error.hpp
include/ncbi-tools++/objtools/edit/edit_exception.hpp
+include/ncbi-tools++/objtools/edit/external_annots.hpp
include/ncbi-tools++/objtools/edit/feattable_edit.hpp
+include/ncbi-tools++/objtools/edit/feature_propagate.hpp
include/ncbi-tools++/objtools/edit/field_handler.hpp
include/ncbi-tools++/objtools/edit/gap_trim.hpp
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