d3c4dd4f1df4b3919520794bfcaac0a7d0935a7f
angie
  Tue Dec 19 12:07:23 2017 -0800
Replace hgTracks' links to NCBI's obsolete Map Viewer with the new & improved Genome Data Viewer.  GDV has only the latest RefSeq assembly for all species except human; it wants GCF_... IDs, which we will have to keep updating in hdb.c.  It's possible that someday NCBI may accept our db IDs instead of GCF_.  refs #18671

diff --git src/hg/hgTracks/extTools.ra src/hg/hgTracks/extTools.ra
index 92f8ce2..6ed54f6 100644
--- src/hg/hgTracks/extTools.ra
+++ src/hg/hgTracks/extTools.ra
@@ -2,64 +2,53 @@
 # Existing URL replacement chars in trackDb, e.g.
 # $s - chrom name, stripping "chr"
 # $S - full chrom name, leaving "chr"
 # $[ - start position of window
 # $start1 - start position of window + 1
 # $] - end position of window
 # $n - current organism name, spaces replaced with underscores
 # $D - current database, like hg19
 
 # Additional ones:
 # $seq - current sequence in view
 # $taxId - taxon id of current db
 # $returnUrl - full URL of current hgTracks page
 # $position - current position, format chr:start-end
 # $halfLen - 1/2 of the current window size (for pointing external tools to the current center)
+# $ncbiGcf - NCBI's RefSeq Assembly (+ annotations) version, e.g. GCF_000001405.25 for hg19
 
 # If something doesn't work, Hit "Esc" when the redirection takes place and append 
 # &debug=1
 # to the URL shown in the browser (it has hgt.redirectTool=xxx in it)
 # This will show all parameters sent to the external site and lets you edit them.
 
 # Note that these configuration entries do not have to be created manually
 # We have a tool "extToolsChromeParse" that can parse the Chrome debug
 # trace to create them automatically from a traced click on a link in Chrome
 # Run the tool "extToolsChromeParse" and look at its help message for details
-tool NCBIPrev
-shortLabel NCBI Map Viewer
-longLabel NCBI Genome Browser
-url https://www.ncbi.nlm.nih.gov/mapview/maps.cgi
-email info@ncbi.nlm.nih.gov
-onlyDbs hg19
-isHttpGet true
-param taxId $taxId
-param CHR $s
-param BEG $start1
-param END $]
-param build previous
 
-tool NCBI
-shortLabel NCBI Map Viewer
-longLabel NCBI Genome Browser
-url https://www.ncbi.nlm.nih.gov/mapview/maps.cgi
+tool GDV
+shortLabel NCBI GDV
+longLabel NCBI Genome Data Viewer
+url https://www.ncbi.nlm.nih.gov/genome/gdv/browser/
 email info@ncbi.nlm.nih.gov
-notDbs hg19
 isHttpGet true
-param taxId $taxId
-param CHR $s
-param BEG $start1
-param END $]
+param id $ncbiGcf
+param chr $s
+param from $start1
+param to $]
+param context genome
 
 tool ensemblArch
 shortLabel Ensembl
 longLabel Ensembl Genome Browser
 url http://dec2014.archive.ensembl.org/$n/contigview
 onlyDbs hg38
 email helpdesk@ensembl.org
 isHttpGet true
 param chr $s
 param start $start1
 param end $]
 
 tool ensembl
 shortLabel Ensembl
 longLabel Ensembl Genome Browser