Make Spack able to apply gz compressed remote patches (#22823)

Modified ncbi-rmblastn to retrieve patches from remote

5 files changed, 31 insertions, 556 deletions

diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index ff41c759ea..b5ce8495e3 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -467,6 +467,8 @@ class URLFetchStrategy(FetchStrategy):
         tarball_container = os.path.join(self.stage.path,
                                          "spack-expanded-archive")
 
+        # Below we assume that the command to decompress expand the
+        # archive in the current working directory
         mkdirp(tarball_container)
         with working_dir(tarball_container):
             decompress(self.archive_file)
diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py
index 2f190e94e1..a1a0e1d6f3 100644
--- a/lib/spack/spack/util/compression.py
+++ b/lib/spack/spack/util/compression.py
@@ -22,6 +22,22 @@ def allowed_archive(path):
     return any(path.endswith(t) for t in ALLOWED_ARCHIVE_TYPES)
 
 
+def _gunzip(archive_file):
+    """Like gunzip, but extracts in the current working directory
+    instead of in-place.
+
+    Args:
+        archive_file (str): absolute path of the file to be decompressed
+    """
+    import gzip
+    decompressed_file = os.path.basename(archive_file.strip('.gz'))
+    working_dir = os.getcwd()
+    destination_abspath = os.path.join(working_dir, decompressed_file)
+    with gzip.open(archive_file, "rb") as f_in:
+        with open(destination_abspath, "wb") as f_out:
+            f_out.write(f_in.read())
+
+
 def decompressor_for(path, extension=None):
     """Get the appropriate decompressor for a path."""
     if ((extension and re.match(r'\.?zip$', extension)) or
@@ -30,8 +46,7 @@ def decompressor_for(path, extension=None):
         unzip.add_default_arg('-q')
         return unzip
     if extension and re.match(r'gz', extension):
-        gunzip = which('gunzip', required=True)
-        return gunzip
+        return _gunzip
     if extension and re.match(r'bz2', extension):
         bunzip2 = which('bunzip2', required=True)
         return bunzip2
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++'