a555f913f8ea500e670e38d03a365ea7c1426fa9
dschmelt
  Wed Jan 19 17:32:57 2022 -0800
Documenting liftOver file size limit part A of refs #28765

diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c
index 1defd9d..984dc0f 100644
--- src/hg/hgLiftOver/hgLiftOver.c
+++ src/hg/hgLiftOver/hgLiftOver.c
@@ -60,39 +60,39 @@
 /* keep the last chain in memory in this format */
 {
 char chainS[64];
 safef(chainS, sizeof(chainS), "%s.%s", chain->fromDb, chain->toDb);
 return cloneString(chainS);
 }
 
 void webMain(struct liftOverChain *chain, boolean multiple, boolean keepSettings, int minSizeQ, 
 	     int minChainT, float minBlocks, float minMatch, boolean fudgeThick)
 /* set up page for entering data */
 {
 struct dbDb *dbList;
 char *fromOrg = hOrganism(chain->fromDb), *toOrg = hOrganism(chain->toDb);
 char *chainString = chainStringVal(chain);
 cgiParagraph(
-    "This tool converts genome coordinates and genome annotation files "
+    "This tool converts genome coordinates and annotation files "
     "between assemblies.  "
-    "The input data can be pasted into the text box or uploaded from a file.  "
-    "For more information, please see our "
+    "The input data can be entered into the text box or uploaded as a file.  "
+    "For files over 500Mb, use the command-line tool described in our "
     "<a href=\"../goldenPath/help/hgTracksHelp.html#Liftover\">LiftOver documentation</a>."
     "&nbsp;&nbsp;If a pair of assemblies cannot be selected from the pull-down menus,"
-    " a sequential lift may still be possible.&nbsp;&nbsp;"
-    "For example, to lift from mm9 to mm39, lift from Mouse mm9 to mm10 and then from"
-    " mm10 to mm39.&nbsp;&nbsp;"
+    " a sequential lift may still be possible (e.g., mm9 to mm10 to mm39).&nbsp;&nbsp;"
+    "If your desired conversion is still not available, please "
+    "<a href=\"../../contacts.html\">contact us</a>."
     "");
 
 /* create HMTL form */
 puts("<FORM ACTION=\"../cgi-bin/hgLiftOver\" METHOD=\"POST\" "
        " ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
 cartSaveSession(cart);
 
 /* create HTML table for layout purposes */
 puts("\n<TABLE WIDTH=\"100%\">\n");
 
 /* top two rows -- genome and assembly menus */
 cgiSimpleTableRowStart();
 cgiTableField("Original Genome: ");
 cgiTableField("Original Assembly: ");
 cgiTableField("New Genome: ");
@@ -304,34 +304,35 @@
 cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:");
 cgiSimpleTableFieldStart();
 printf("%s", fudgeThick ? "on" : "off");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiTableEnd();
 }
 
 void webDownloads()
 {
 webNewSection("Command Line Tool");
 cgiParagraph(
 "To lift genome annotations locally on Linux systems, download the "
 "<A HREF=\"https://genome-store.ucsc.edu\">" 
-"<I>liftOver</I></A> executable and the appropriate "
+"<I>LiftOver</I></A> executable and the appropriate "
 "<A HREF=\"http://hgdownload.soe.ucsc.edu/downloads.html#liftover\">"
 "chain file</A>."
-" Run <I>liftOver</I> with no arguments to see the usage message.\n");
+" Run <I>liftOver</I> with no arguments to see the usage message.\n"
+"See the <a href=\"../goldenPath/help/hgTracksHelp.html#Liftover\">LiftOver documentation</a>.");
 }
 
 
 double scoreLiftOverChain(struct liftOverChain *chain,
     char *fromOrg, char *fromDb, char *toOrg, char *toDb,
     char *cartOrg, char *cartDb, struct hash *dbRank, 
     struct hash *dbHash)
 /* Score the chain in terms of best match for cart settings */
 {
 double score = 0;
 struct dbDb *chainFromDbDb = hashFindVal(dbHash, chain->fromDb);
 struct dbDb *chainToDbDb = hashFindVal(dbHash, chain->toDb);
 
 char *chainFromOrg = (chainFromDbDb) ? chainFromDbDb->organism : NULL;
 char *chainToOrg = (chainToDbDb) ? chainToDbDb->organism : NULL;