7d91e54c881a55a9cedd45786a668b165e284667
galt
  Fri Jan 25 18:52:31 2013 -0800
Added detailed description of how paths are handled between gfServer commandline and the various clients that use gfServer.
diff --git src/gfServer/gfServer.c src/gfServer/gfServer.c
index 53c87c0..6a8b4b6 100644
--- src/gfServer/gfServer.c
+++ src/gfServer/gfServer.c
@@ -104,30 +104,41 @@
   "   -syslog    Log to syslog\n"
   "   -logFacility=facility log to the specified syslog facility - default local0.\n"
   "   -mask      Use masking from nib file.\n"
   "   -repMatch=N Number of occurrences of a tile (nmer) that trigger repeat masking the tile.\n"
   "               Default is %d.\n"
   "   -maxDnaHits=N Maximum number of hits for a dna query that are sent from the server.\n"
   "               Default is %d.\n"
   "   -maxTransHits=N Maximum number of hits for a translated query that are sent from the server.\n"
   "               Default is %d.\n"
   "   -maxNtSize=N Maximum size of untranslated DNA query sequence\n"
   "               Default is %d\n"
   "   -maxAaSize=N Maximum size of protein or translated DNA queries\n"
   "               Default is %d\n"
   "   -canStop If set then a quit message will actually take down the\n"
   "            server\n"
+  "Note about file(s) specified in the start command:\n"
+  "    The path(s) specified here are sent back exactly as-is\n"
+  "    to clients such as gfClient, hgBlat, webBlat.\n"
+  "    It is intended that relative paths are used.\n"
+  "    Absolute paths starting with '/' tend not to work\n"
+  "    unless the client is on the same machine as the server.\n"
+  "    For use with hgBlat and webBlat, cd to the directory where the file is\n"
+  "    and use the plain file name with no slashes.\n"
+  "      hgBlat will append the path(s) given to dbDb.nibPath.\n"
+  "     webBlat will append the path(s) given to path specified in webBlat.cfg.\n"
+  "    gfClient will append the path(s) given to the seqDir path specified.\n"
   ,	gfVersion, repMatch, maxDnaHits, maxTransHits, maxNtSize, maxAaSize
   );
 
 }
 
 void genoFindDirect(char *probeName, int fileCount, char *seqFiles[])
 /* Don't set up server - just directly look for matches. */
 {
 struct genoFind *gf = NULL;
 struct lineFile *lf = lineFileOpen(probeName, TRUE);
 struct dnaSeq seq;
 int hitCount = 0, clumpCount = 0, oneHit;
 ZeroVar(&seq);
 
 if (doTrans)