cff386c4731971ed35c2a379135a6387d8bf0c9f
dschmelt
  Thu Mar 10 16:33:41 2022 -0800
Panel App track engineering refs #25568

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index 8f065f8..1fe1747 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -6954,17 +6954,41 @@
         remap.hg38.hg19.chain
 #real    9m31.900s
 #user    9m1.624s
 #sys     0m20.863s
     hgLoadChain hg38 -tIndex chainHg19ReMap remap.hg38.hg19.chain
 #Loading 5315 chains into hg38.chainHg19ReMap
     time axtChain -psl -linearGap=medium -verbose=0 remap.hg38.hg19.psl \
       /hive/data/genomes/hg38/hg38.2bit /hive/data/genomes/hg19/hg19.2bit \
       remap.axtChain.hg38.hg19.chain
 #real    2m26.333s
 #user    2m4.237s
 #sys     0m22.071s
     hgLoadChain hg38 -tIndex chainHg19ReMapAxtChain remap.axtChain.hg38.hg19.chain
 #Loading 2115 chains into hg38.chainHg19ReMapAxtChain
 
+###################################################
+
+# PanelApp refs #25568
+cd /hive/data/genomes/hg38/bed
+mkdir panelApp
+cd panelApp
+wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/panel_hg38.bb
+wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/str_hg38.bb
+mv /cluster/home/bnguy/trackhub/region/region_hg38.bb .
+mv panel_hg38.bb genesPanel.bb
+mv str_hg38.bb STRsPanel.bb
+mv region_hg38.bb CNVregions.bb
+cd /gbdb/hg38
+mkdir panelApp
+cd panelApp
+ln -s /hive/data/genomes/hg38/bed/panelApp/genesPanel.bb
+ln -s /hive/data/genomes/hg38/bed/panelApp/STRsPanel.bb
+ln -s /hive/data/genomes/hg38/bed/panelApp/CNVregions.bb 
+cd ~/kent/src/hg/makeDb/trackDb/human/hg38
+wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/panelapp.html
+mv panelapp.html panelApp.html
+curl https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/trackDb.txt >> trackDb.ra
+vi trackDb.ra
+cd ~/kent/src/hg/makeDb/trackDb
+make alpha DBS=hg38
 
-#########################################################################