diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.9.0+-rmblast-p1.patch | 238 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/ncbi-rmblastn/package.py | 16 |
2 files changed, 251 insertions, 3 deletions
diff --git a/var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.9.0+-rmblast-p1.patch b/var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.9.0+-rmblast-p1.patch new file mode 100644 index 0000000000..6dd66369e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.9.0+-rmblast-p1.patch @@ -0,0 +1,238 @@ +diff -rupN ncbi-blast-2.9.0+-src.orig/c++/src/app/rmblastn/Makefile.in ncbi-blast-2.9.0+-src/c++/src/app/rmblastn/Makefile.in +--- ncbi-blast-2.9.0+-src.orig/c++/src/app/rmblastn/Makefile.in 1969-12-31 16:00:00.000000000 -0800 ++++ ncbi-blast-2.9.0+-src/c++/src/app/rmblastn/Makefile.in 2019-04-01 13:25:24.854320235 -0700 +@@ -0,0 +1,16 @@ ++# $Id: Makefile.in 371962 2012-08-14 09:45:56Z coulouri $ ++ ++# Meta-makefile("APP" project) ++################################# ++ ++REQUIRES = objects algo ++ ++APP_PROJ = rmblastn ++ ++srcdir = @srcdir@ ++include @builddir@/Makefile.meta ++ ++.PHONY: all $(APP_PROJ) ++ ++rmblastn: ++ ${MAKE} ${MFLAGS} -f Makefile.rmblastn_app +diff -rupN ncbi-blast-2.9.0+-src.orig/c++/src/app/rmblastn/Makefile.rmblastn.app ncbi-blast-2.9.0+-src/c++/src/app/rmblastn/Makefile.rmblastn.app +--- ncbi-blast-2.9.0+-src.orig/c++/src/app/rmblastn/Makefile.rmblastn.app 1969-12-31 16:00:00.000000000 -0800 ++++ ncbi-blast-2.9.0+-src/c++/src/app/rmblastn/Makefile.rmblastn.app 2019-04-01 13:25:24.856320218 -0700 +@@ -0,0 +1,16 @@ ++WATCHERS = camacho madden maning ++ ++APP = rmblastn ++SRC = rmblastn_app ++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) ++LIB = blast_app_util $(LIB_:%=%$(STATIC)) ++ ++# De-universalize Mac builds to work around a PPC toolchain limitation ++CFLAGS = $(FAST_CFLAGS:ppc=i386) ++CXXFLAGS = $(FAST_CXXFLAGS:ppc=i386) ++LDFLAGS = $(FAST_LDFLAGS:ppc=i386) ++ ++CPPFLAGS = $(ORIG_CPPFLAGS) ++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) ++ ++REQUIRES = objects -Cygwin +diff -rupN ncbi-blast-2.9.0+-src.orig/c++/src/app/rmblastn/rmblastn_app.cpp ncbi-blast-2.9.0+-src/c++/src/app/rmblastn/rmblastn_app.cpp +--- ncbi-blast-2.9.0+-src.orig/c++/src/app/rmblastn/rmblastn_app.cpp 1969-12-31 16:00:00.000000000 -0800 ++++ ncbi-blast-2.9.0+-src/c++/src/app/rmblastn/rmblastn_app.cpp 2019-04-01 13:25:24.858320200 -0700 +@@ -0,0 +1,183 @@ ++/* $Id: rmblastn_app.cpp 371962 2012-08-14 09:45:56Z coulouri $ ++ * =========================================================================== ++ * ++ * PUBLIC DOMAIN NOTICE ++ * ++ * =========================================================================== ++ * ++ * Authors: Robert M. Hubley ++ * Christiam Camacho ( original blastn_app.cpp ) ++ * ++ */ ++ ++/** @file rmblastn_app.cpp ++ * RMBLASTN command line application ++ */ ++ ++#ifndef SKIP_DOXYGEN_PROCESSING ++static char const rcsid[] = ++ "$Id: rmblastn_app.cpp 371962 2012-08-14 09:45:56Z coulouri $"; ++#endif /* SKIP_DOXYGEN_PROCESSING */ ++ ++#include <ncbi_pch.hpp> ++#include <corelib/ncbiapp.hpp> ++#include <algo/blast/api/local_blast.hpp> ++#include <algo/blast/api/remote_blast.hpp> ++#include <algo/blast/blastinput/blast_fasta_input.hpp> ++#include <algo/blast/blastinput/rmblastn_args.hpp> ++#include <algo/blast/api/objmgr_query_data.hpp> ++#include <algo/blast/format/blast_format.hpp> ++#include "../blast/blast_app_util.hpp" ++ ++#ifndef SKIP_DOXYGEN_PROCESSING ++USING_NCBI_SCOPE; ++USING_SCOPE(blast); ++USING_SCOPE(objects); ++#endif ++ ++class CRMBlastnApp : public CNcbiApplication ++{ ++public: ++ /** @inheritDoc */ ++ CRMBlastnApp() { ++ CRef<CVersion> version(new CVersion()); ++ version->SetVersionInfo(new CBlastVersion()); ++ SetFullVersion(version); ++ } ++private: ++ /** @inheritDoc */ ++ virtual void Init(); ++ /** @inheritDoc */ ++ virtual int Run(); ++ ++ /// This application's command line args ++ CRef<CRMBlastnAppArgs> m_CmdLineArgs; ++}; ++ ++ ++ ++void CRMBlastnApp::Init() ++{ ++ // formulate command line arguments ++ m_CmdLineArgs.Reset(new CRMBlastnAppArgs()); ++ ++ // read the command line ++ ++ HideStdArgs(fHideLogfile | fHideConffile | fHideFullVersion | fHideXmlHelp | fHideDryRun); ++ SetupArgDescriptions(m_CmdLineArgs->SetCommandLine()); ++} ++ ++int CRMBlastnApp::Run(void) ++{ ++ int status = BLAST_EXIT_SUCCESS; ++ ++ try { ++ ++ // Allow the fasta reader to complain on invalid sequence input ++ SetDiagPostLevel(eDiag_Warning); ++ ++ /*** Get the BLAST options ***/ ++ const CArgs& args = GetArgs(); ++ CRef<CBlastOptionsHandle> opts_hndl; ++ if(RecoverSearchStrategy(args, m_CmdLineArgs)) { ++ opts_hndl.Reset(&*m_CmdLineArgs->SetOptionsForSavedStrategy(args)); ++ } ++ else { ++ opts_hndl.Reset(&*m_CmdLineArgs->SetOptions(args)); ++ } ++ const CBlastOptions& opt = opts_hndl->GetOptions(); ++ ++ /*** Get the query sequence(s) ***/ ++ CRef<CQueryOptionsArgs> query_opts = ++ m_CmdLineArgs->GetQueryOptionsArgs(); ++ SDataLoaderConfig dlconfig(query_opts->QueryIsProtein()); ++ dlconfig.OptimizeForWholeLargeSequenceRetrieval(); ++ CBlastInputSourceConfig iconfig(dlconfig, query_opts->GetStrand(), ++ query_opts->UseLowercaseMasks(), ++ query_opts->GetParseDeflines(), ++ query_opts->GetRange()); ++ iconfig.SetSkipSeqCheck(true); ++ CBlastFastaInputSource fasta(m_CmdLineArgs->GetInputStream(), iconfig); ++ CBlastInput input(&fasta, m_CmdLineArgs->GetQueryBatchSize()); ++ ++ /*** Initialize the database/subject ***/ ++ CRef<CBlastDatabaseArgs> db_args(m_CmdLineArgs->GetBlastDatabaseArgs()); ++ CRef<CLocalDbAdapter> db_adapter; ++ CRef<CScope> scope; ++ InitializeSubject(db_args, opts_hndl, m_CmdLineArgs->ExecuteRemotely(), ++ db_adapter, scope); ++ _ASSERT(db_adapter && scope); ++ ++ // Initialize the megablast database index now so we can know whether an indexed search will be run. ++ // This is only important for the reference in the report, but would be done anyway. ++ if (opt.GetUseIndex() && !m_CmdLineArgs->ExecuteRemotely()) { ++ CRef<CBlastOptions> my_options(&(opts_hndl->SetOptions())); ++ CSetupFactory::InitializeMegablastDbIndex(my_options); ++ } ++ ++ /*** Get the formatting options ***/ ++ CRef<CFormattingArgs> fmt_args(m_CmdLineArgs->GetFormattingArgs()); ++ CBlastFormat formatter(opt, *db_adapter, ++ fmt_args->GetFormattedOutputChoice(), ++ query_opts->GetParseDeflines(), ++ m_CmdLineArgs->GetOutputStream(), ++ fmt_args->GetNumDescriptions(), ++ fmt_args->GetNumAlignments(), ++ *scope, ++ opt.GetMatrixName(), ++ fmt_args->ShowGis(), ++ fmt_args->DisplayHtmlOutput(), ++ opt.GetQueryGeneticCode(), ++ opt.GetDbGeneticCode(), ++ opt.GetSumStatisticsMode(), ++ m_CmdLineArgs->ExecuteRemotely(), ++ db_adapter->GetFilteringAlgorithm(), ++ fmt_args->GetCustomOutputFormatSpec(), ++ m_CmdLineArgs->GetTask() == "megablast", ++ opt.GetMBIndexLoaded()); ++ ++ ++ formatter.PrintProlog(); ++ ++ /*** Process the input ***/ ++ for (; !input.End(); formatter.ResetScopeHistory()) { ++ ++ CRef<CBlastQueryVector> query_batch(input.GetNextSeqBatch(*scope)); ++ CRef<IQueryFactory> queries(new CObjMgr_QueryFactory(*query_batch)); ++ ++ SaveSearchStrategy(args, m_CmdLineArgs, queries, opts_hndl); ++ ++ CRef<CSearchResultSet> results; ++ ++ if (m_CmdLineArgs->ExecuteRemotely()) { ++ CRef<CRemoteBlast> rmt_blast = ++ InitializeRemoteBlast(queries, db_args, opts_hndl, ++ m_CmdLineArgs->ProduceDebugRemoteOutput()); ++ results = rmt_blast->GetResultSet(); ++ } else { ++ CLocalBlast lcl_blast(queries, opts_hndl, db_adapter); ++ lcl_blast.SetNumberOfThreads(m_CmdLineArgs->GetNumThreads()); ++ results = lcl_blast.Run(); ++ } ++ ++ ITERATE(CSearchResultSet, result, *results) { ++ formatter.PrintOneResultSet(**result, query_batch); ++ } ++ } ++ ++ formatter.PrintEpilog(opt); ++ ++ if (m_CmdLineArgs->ProduceDebugOutput()) { ++ opts_hndl->GetOptions().DebugDumpText(NcbiCerr, "BLAST options", 1); ++ } ++ ++ } CATCH_ALL(status) ++ return status; ++} ++ ++#ifndef SKIP_DOXYGEN_PROCESSING ++int main(int argc, const char* argv[] /*, const char* envp[]*/) ++{ ++ return CRMBlastnApp().AppMain(argc, argv, 0, eDS_Default, 0); ++} ++#endif /* SKIP_DOXYGEN_PROCESSING */ + +--- ncbi-blast-2.9.0+-src.orig/c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp 2019-08-02 15:07:03.643749527 -0700 ++++ ncbi-blast-2.9.0+-src/c++/src/objtools/blast/seqdb_reader/seqdbimpl.cpp 2019-08-02 15:07:05.839730395 -0700 +@@ -808,7 +808,6 @@ + if (! m_OidListSetup) { + x_GetOidList(locked); + } +- m_Atlas.Unlock(locked); + + if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { + return vol->GetSeqIDs(vol_oid); diff --git a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py index a8a9727cad..b23f616163 100644 --- a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py +++ b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py @@ -9,9 +9,19 @@ from spack import * class NcbiRmblastn(AutotoolsPackage): """RMBlast search engine for NCBI""" - homepage = "https://www.ncbi.nlm.nih.gov/" - url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/LATEST/ncbi-rmblastn-2.2.28-src.tar.gz" + homepage = "http://www.repeatmasker.org/RMBlast.html" + url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-src.tar.gz" - version('2.2.28', 'fb5f4e2e02ffcb1b17af2e9f206c5c22') + version('2.9.0', 'e6a44564e6278c445826ec2720f104b4') + patch('isb-2.9.0+-rmblast-p1.patch', when="@2.9.0") configure_directory = 'c++' + + def configure_args(self): + args = [ + "--with-mt", + "--without-debug", + "--without-krb5", + "--without-openssl", + "--with-projects=scripts/projects/rmblastn/project.lst"] + return args |