0c551e8432f5c9bbf86ac83e49a5c640ae7dbc55
angie
  Fri Jun 2 11:40:19 2023 -0700
Add support for a couple Influenza A RefSeq assemblies -- only for segment 4 (HA gene, the "H" in serotypes like "H3N2") for now since we'll need another menu (or smart matching) in order to support all segments.

diff --git src/hg/hgPhyloPlace/phyloPlaceMain.c src/hg/hgPhyloPlace/phyloPlaceMain.c
index 7dc9755..07b51be 100644
--- src/hg/hgPhyloPlace/phyloPlaceMain.c
+++ src/hg/hgPhyloPlace/phyloPlaceMain.c
@@ -1,22 +1,26 @@
 /* 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 "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"
   "   -db=D                db (default: wuhCor1)\n"
   "   -protobuf=F          Protobuf (from first column of protobufs.tab, with hgPhyloPlaceData/db\n"
   "                        prepended; default: value from first line)\n"
   "   -subtreeSize=N       Value to pass to usher option --print-subtrees-size\n"
   );
@@ -31,22 +35,36 @@
 };
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 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();
+
+if (isHubTrack(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, db, protobuf, TRUE, subtreeSize, 9, &success);
 if (ctFile)
     printf("ctFile = %s\n", ctFile);
 else
     printf("no ctFile.\n");
 return (success == TRUE);
 }