From 5b12568c4f17fb9914be9e903eff3aad007049ef Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Date: Wed, 28 Apr 2021 17:00:58 +0200
Subject: Make Spack able to apply gz compressed remote patches (#22823)
Modified ncbi-rmblastn to retrieve patches from remote
---
.../ncbi-rmblastn/isb-2.11.0+-rmblast.patch | 314 ---------------------
.../ncbi-rmblastn/isb-2.9.0+-rmblast-p1.patch | 238 ----------------
.../builtin/packages/ncbi-rmblastn/package.py | 14 +-
3 files changed, 12 insertions(+), 554 deletions(-)
delete mode 100644 var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.11.0+-rmblast.patch
delete mode 100644 var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.9.0+-rmblast-p1.patch
(limited to 'var')
diff --git a/var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.11.0+-rmblast.patch b/var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.11.0+-rmblast.patch
deleted file mode 100644
index 0ca0ef47c9..0000000000
--- a/var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.11.0+-rmblast.patch
+++ /dev/null
@@ -1,314 +0,0 @@
-diff -rupN ncbi-blast-2.11.0+-src.orig/c++/src/algo/blast/format/blast_format.cpp ncbi-blast-2.11.0+-src/c++/src/algo/blast/format/blast_format.cpp
---- ncbi-blast-2.11.0+-src.orig/c++/src/algo/blast/format/blast_format.cpp 2020-09-28 11:27:07.000000000 -0700
-+++ ncbi-blast-2.11.0+-src/c++/src/algo/blast/format/blast_format.cpp 2021-02-09 13:45:03.737153875 -0800
-@@ -2463,13 +2463,6 @@ void CBlastFormat::LogBlastSearchInfo(CB
- }
- }
- else {
-- string dir = kEmptyStr;
-- CFile::SplitPath(m_DbName, &dir);
-- string db_name = m_DbName;
-- if (dir != kEmptyStr) {
-- db_name = m_DbName.substr(dir.length());
-- }
-- report.AddParam(CBlastUsageReport::eDBName, db_name);
- report.AddParam(CBlastUsageReport::eDBLength, GetDbTotalLength());
- report.AddParam(CBlastUsageReport::eDBNumSeqs, num_seqs);
- report.AddParam(CBlastUsageReport::eDBDate, m_DbInfo[0].date);
-diff -rupN ncbi-blast-2.11.0+-src.orig/c++/src/app/blast/blast_app_util.cpp ncbi-blast-2.11.0+-src/c++/src/app/blast/blast_app_util.cpp
---- ncbi-blast-2.11.0+-src.orig/c++/src/app/blast/blast_app_util.cpp 2020-08-31 08:38:53.000000000 -0700
-+++ ncbi-blast-2.11.0+-src/c++/src/app/blast/blast_app_util.cpp 2021-02-09 13:43:55.672814151 -0800
-@@ -964,12 +964,6 @@ void LogRPSCmdOptions(blast::CBlastUsage
- args.GetBlastDatabaseArgs()->GetSearchDatabase()->GetSeqDb().NotEmpty()) {
-
- CRef<CSeqDB> db = args.GetBlastDatabaseArgs()->GetSearchDatabase()->GetSeqDb();
-- string db_name = db->GetDBNameList();
-- int off = db_name.find_last_of(CFile::GetPathSeparator());
-- if (off != -1) {
-- db_name.erase(0, off+1);
-- }
-- report.AddParam(CBlastUsageReport::eDBName, db_name);
- report.AddParam(CBlastUsageReport::eDBLength, (Int8) db->GetTotalLength());
- report.AddParam(CBlastUsageReport::eDBNumSeqs, db->GetNumSeqs());
- report.AddParam(CBlastUsageReport::eDBDate, db->GetDate());
-diff -rupN ncbi-blast-2.11.0+-src.orig/c++/src/app/blastdb/blastdbcmd.cpp ncbi-blast-2.11.0+-src/c++/src/app/blastdb/blastdbcmd.cpp
---- ncbi-blast-2.11.0+-src.orig/c++/src/app/blastdb/blastdbcmd.cpp 2020-09-22 06:14:39.000000000 -0700
-+++ ncbi-blast-2.11.0+-src/c++/src/app/blastdb/blastdbcmd.cpp 2021-02-09 13:45:40.331798879 -0800
-@@ -1186,12 +1186,6 @@ void CBlastDBCmdApp::x_AddCmdOptions()
- }
-
-
-- string db_name = m_BlastDb->GetDBNameList();
-- int off = db_name.find_last_of(CFile::GetPathSeparator());
-- if (off != -1) {
-- db_name.erase(0, off+1);
-- }
-- m_UsageReport.AddParam(CBlastUsageReport::eDBName, db_name);
- m_UsageReport.AddParam(CBlastUsageReport::eDBLength, (Int8) m_BlastDb->GetTotalLength());
- m_UsageReport.AddParam(CBlastUsageReport::eDBNumSeqs, m_BlastDb->GetNumSeqs());
- m_UsageReport.AddParam(CBlastUsageReport::eDBDate, m_BlastDb->GetDate());
-diff -rupN ncbi-blast-2.11.0+-src.orig/c++/src/app/rmblastn/Makefile.in ncbi-blast-2.11.0+-src/c++/src/app/rmblastn/Makefile.in
---- ncbi-blast-2.11.0+-src.orig/c++/src/app/rmblastn/Makefile.in 1969-12-31 16:00:00.000000000 -0800
-+++ ncbi-blast-2.11.0+-src/c++/src/app/rmblastn/Makefile.in 2021-02-09 13:00:33.072893864 -0800
-@@ -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-2.11.0+-src.orig/c++/src/app/rmblastn/Makefile.rmblastn.app ncbi-blast-2.11.0+-src/c++/src/app/rmblastn/Makefile.rmblastn.app
---- ncbi-blast-2.11.0+-src.orig/c++/src/app/rmblastn/Makefile.rmblastn.app 1969-12-31 16:00:00.000000000 -0800
-+++ ncbi-blast-2.11.0+-src/c++/src/app/rmblastn/Makefile.rmblastn.app 2021-02-09 13:00:33.072893864 -0800
-@@ -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-2.11.0+-src.orig/c++/src/app/rmblastn/rmblastn_app.cpp ncbi-blast-2.11.0+-src/c++/src/app/rmblastn/rmblastn_app.cpp
---- ncbi-blast-2.11.0+-src.orig/c++/src/app/rmblastn/rmblastn_app.cpp 1969-12-31 16:00:00.000000000 -0800
-+++ ncbi-blast-2.11.0+-src/c++/src/app/rmblastn/rmblastn_app.cpp 2021-02-09 13:55:13.371077793 -0800
-@@ -0,0 +1,197 @@
-+/* $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
-+ */
-+
-+#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);
-+ m_StopWatch.Start();
-+ if (m_UsageReport.IsEnabled()) {
-+ m_UsageReport.AddParam(CBlastUsageReport::eVersion, GetVersion().Print());
-+ }
-+ }
-+
-+ ~CRMBlastnApp() {
-+ m_UsageReport.AddParam(CBlastUsageReport::eRunTime, m_StopWatch.Elapsed());
-+ }
-+private:
-+ /** @inheritDoc */
-+ virtual void Init();
-+ /** @inheritDoc */
-+ virtual int Run();
-+
-+ /// This application's command line args
-+ CRef<CRMBlastnAppArgs> m_CmdLineArgs;
-+ CBlastUsageReport m_UsageReport;
-+ CStopWatch m_StopWatch;
-+};
-+
-+
-+
-+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();
-+
-+ /*** 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);
-+
-+ /*** 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 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);
-+ }
-+
-+ LogQueryInfo(m_UsageReport, input);
-+ formatter.LogBlastSearchInfo(m_UsageReport);
-+ } CATCH_ALL(status)
-+
-+ // The program and task name are overwritten here to avoid changing the
-+ // "true" values of Program and Task everywhere else in the program
-+ m_UsageReport.AddParam(CBlastUsageReport::eProgram, (string) "rmblastn");
-+ m_UsageReport.AddParam(CBlastUsageReport::eTask, (string) "rmblastn");
-+
-+ m_UsageReport.AddParam(CBlastUsageReport::eNumThreads, (int) m_CmdLineArgs->GetNumThreads());
-+ m_UsageReport.AddParam(CBlastUsageReport::eExitStatus, status);
-+ return status;
-+}
-+
-+#ifndef SKIP_DOXYGEN_PROCESSING
-+int NcbiSys_main(int argc, ncbi::TXChar* argv[])
-+{
-+ return CRMBlastnApp().AppMain(argc, argv);
-+}
-+#endif /* SKIP_DOXYGEN_PROCESSING */
-diff -rupN ncbi-blast-2.11.0+-src.orig/c++/src/connect/ncbi_usage_report.cpp ncbi-blast-2.11.0+-src/c++/src/connect/ncbi_usage_report.cpp
---- ncbi-blast-2.11.0+-src.orig/c++/src/connect/ncbi_usage_report.cpp 2020-03-03 10:47:23.000000000 -0800
-+++ ncbi-blast-2.11.0+-src/c++/src/connect/ncbi_usage_report.cpp 2021-02-23 15:38:56.089137179 -0800
-@@ -46,7 +46,7 @@ BEGIN_NCBI_SCOPE
- // All parameters can be redefined in the configuration file.
-
- // Default "pinger" CGI url for reporting statistics.
--const char* kDefault_URL = "https://www.ncbi.nlm.nih.gov/stat";
-+const char* kDefault_URL = "https://www.repeatmasker.org/rmblast/stat";
-
- // Usage logging is disabled by default.
- const bool kDefault_IsEnabled = false;
-@@ -265,11 +265,6 @@ void CUsageReportJob::x_CopyFrom(const C
-
- static string s_GetOS()
- {
-- // Check NCBI_OS first, configure can define OS name already
--#if defined(NCBI_OS)
-- return NCBI_OS;
--#endif
-- // Fallback, try to guess
- #if defined(_WIN32)
- return "MSWIN"; // Windows
- #elif defined(__CYGWIN__)
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
deleted file mode 100644
index 6dd66369e5..0000000000
--- a/var/spack/repos/builtin/packages/ncbi-rmblastn/isb-2.9.0+-rmblast-p1.patch
+++ /dev/null
@@ -1,238 +0,0 @@
-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 3641ece033..e7ef8bf897 100644
--- a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py
+++ b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py
@@ -22,8 +22,18 @@ class NcbiRmblastn(AutotoolsPackage):
# isb-2.11.0+-rmblast.patch.gz
# The patch is downloaded and unzipped in the ncbi-rmblastn Spack package
# directory to make it available for the patch directive.
- patch('isb-2.11.0+-rmblast.patch', when="@2.11.0")
- patch('isb-2.9.0+-rmblast-p1.patch', when="@2.9.0")
+ patch(
+ 'http://www.repeatmasker.org/isb-2.11.0+-rmblast.patch.gz',
+ sha256='ce985abd3512834adb9ad3e4078fbf9608a33a2ee6538a1e94b641490c92f899',
+ archive_sha256='0fc27781c2ea2f17645247e2f3775b5d18c56f0b62761a865347be745ea4f6be',
+ when='@2.11.0'
+ )
+ patch(
+ 'http://www.repeatmasker.org/isb-2.9.0+-rmblast.patch.gz',
+ sha256='ffa0845801aed11f4215b452532f3ff5b3dcb49ac8c14169568aaa585b9450ed',
+ archive_sha256='e746ee480ade608052306fd21f015c8a323f27029f65399275216f9a4c882d59',
+ when='@2.9.0'
+ )
configure_directory = 'c++'
--
cgit v1.2.3-70-g09d2