87a162ccdc3ac94525fc1011dec5bc10e2cf2171
markd
  Thu Jul 2 16:12:57 2020 -0700
web blat working

diff --git src/gfServer/gfServer.c src/gfServer/gfServer.c
index 172d2e0..9c5ed66 100644
--- src/gfServer/gfServer.c
+++ src/gfServer/gfServer.c
@@ -95,33 +95,33 @@
   "      gfServer pcrDirect fPrimer rPrimer file(s).2bit\n"
   "   To figure out usage level:\n"
   "      gfServer status host port\n"
   "   To get input file list:\n"
   "      gfServer files host port\n"
   "   To generate a precomputed index:\n"
   "      gfServer index gfidx file(s)\n"
   "     where the files are .2bit or .nib format files.  Separate indexes must be created\n"
   "     for untranslated and translated queries.  These can be used with a persistent server\n"
   "     as with 'start -indexFile or a dynamic server. They must follow the naming convention for\n"
   "     for dynamic servers.\n"
   "   To run a dynamic server (usually called by xinet):\n"
   "      gfServer dynserver rootdir\n"
   "     The root directory must contain directories for each genome with the twobit and index\n"
   "     files following the convention:\n"
-  "         $genome/$genome.2bit\n"
-  "         $genome/$genome.untrans.gfidx\n"
-  "         $genome/$genome.trans.gfidx\n"
+  "         $rootdir/$genome/$genome.2bit\n"
+  "         $rootdir/$genome/$genome.untrans.gfidx\n"
+  "         $rootdir/$genome/$genome.trans.gfidx\n"
   "     Both indexes must exist.\n"
   "\n"
   "options:\n"
   "   -tileSize=N     Size of n-mers to index.  Default is 11 for nucleotides, 4 for\n"
   "                   proteins (or translated nucleotides).\n"
   "   -stepSize=N     Spacing between tiles. Default is tileSize.\n"
   "   -minMatch=N     Number of n-mer matches that trigger detailed alignment.\n"
   "                   Default is 2 for nucleotides, 3 for proteins.\n"
   "   -maxGap=N       Number of insertions or deletions allowed between n-mers.\n"
   "                   Default is 2 for nucleotides, 0 for proteins.\n"
   "   -trans          Translate database to protein in 6 frames.  Note: it is best\n"
   "                   to run this on RepeatMasked data in this case.\n"
   "   -log=logFile    Keep a log file that records server requests.\n"
   "   -seqLog         Include sequences in log file (not logged with -syslog).\n"
   "   -ipLog          Include user's IP in log file (not logged with -syslog).\n"