0114df80d5034a730eeb50f04fca0afe73af3dce
angie
  Tue Dec 5 13:51:41 2023 -0800
When db is really a db/hub, use it as db not just refName.

diff --git src/hg/hgPhyloPlace/phyloPlaceMain.c src/hg/hgPhyloPlace/phyloPlaceMain.c
index bcbbc19..95acda9 100644
--- src/hg/hgPhyloPlace/phyloPlaceMain.c
+++ src/hg/hgPhyloPlace/phyloPlaceMain.c
@@ -1,21 +1,22 @@
 /* phyloPlace: place SARS-CoV-2 sequences in phylogenetic tree using add_missing_samples program. */
 
 /* Copyright (C) 2020-2022 The Regents of the University of California */
 
 #include "common.h"
 #include "cart.h"
+#include "hdb.h"
 #include "knetUdc.h"
 #include "linefile.h"
 #include "options.h"
 #include "trackHub.h"
 #include "hubConnect.h"
 #include "phyloPlace.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "phyloPlace - Place SARS-CoV-2 sequences in phylogenetic tree using add_missing_samples program\n"
   "usage:\n"
   "   phyloPlace file.[fa|vcf]\n"
   "options:\n"
@@ -41,30 +42,36 @@
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 char *userSeqOrVcf = argv[1];
 struct lineFile *lf = lineFileOpen(userSeqOrVcf, TRUE);
 char *db = optionVal("db", "wuhCor1");
 char *protobuf = optionVal("protobuf", NULL);
 int subtreeSize = optionInt("subtreeSize", 50);
 boolean success = FALSE;
 
 int timeout = 300;
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
+char *realDb = NULL;
 if (isHubTrack(db))
     {
+    realDb = db;
     // Connect to hubs so phyloPlaceSamples doesn't croak later.
     struct cart *cart = cartOfNothing();
     struct slName *supportedDbs = phyloPlaceDbList(cart);
     if (! slNameInList(supportedDbs, db))
         errAbort("Can't find db '%s'", db);
     }
-char *ctFile = phyloPlaceSamples(lf, "hg38", db, protobuf, TRUE, subtreeSize, 9, &success);
+else if (hDbExists(db))
+    realDb = db;
+else
+    realDb = "hg38";
+char *ctFile = phyloPlaceSamples(lf, realDb, db, protobuf, TRUE, subtreeSize, 9, &success);
 if (ctFile)
     printf("ctFile = %s\n", ctFile);
 else
     printf("no ctFile.\n");
 return (success == TRUE);
 }