e5d37503f652d47a0d2e5c6a03562cdf6442736b
braney
  Mon May 30 09:55:25 2022 -0700
some tweaks to chm13 to get searchTrix to work

diff --git src/hg/makeDb/doc/chm13/initial.txt src/hg/makeDb/doc/chm13/initial.txt
index 9661358..97b5fc1 100644
--- src/hg/makeDb/doc/chm13/initial.txt
+++ src/hg/makeDb/doc/chm13/initial.txt
@@ -1,33 +1,38 @@
 mkdir /hive/data/genomes/chm13
 cd /hive/data/genomes/chm13
 mkdir /gbdb/chm13
 wget "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.2bit" -O chm13.2bit
 ln -s `pwd`/chm13.2bit /gbdb/chm13/chm13.2bit
 mkdir hubs
 cd hubs
 ln -s /hive/data/genomes/chm13/hubs /gbdb/chm13/hubs
 
 ln -s /usr/local/apache/htdocs-hgdownload/hubs/GCA/009/914/755/GCA_009914755.4/bbi /gbdb/chm13/bbi
+ln -s /usr/local/apache/htdocs-hgdownload/hubs/GCA/009/914/755/GCA_009914755.4/ixIxx /gbdb/chm13/ixIxx
 
 wget "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chromAlias.txt"
 wget "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/groups.txt"
 
 # get hub and genomes stanza from existing hub
 wget "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt" -O - | raToLines /dev/stdin /dev/stdout | egrep "^hub|^genome" | linesToRa /dev/stdin hubAndGenome.txt
 
 mkdir ~/kent/src/hg/makeDb/trackDb/human/chm13
 cd  ~/kent/src/hg/makeDb/trackDb/human/chm13
-wget "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt" -O - | raToLines /dev/stdin /dev/stdout | egrep -v "^hub|^genome|^include" | linesToRa /dev/stdin /dev/stdout | sed 's?bigDataUrl ?& /gbdb/chm13/?' > trackDb.ra
+wget "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt" -O - | raToLines /dev/stdin /dev/stdout | egrep -v "^hub|^genome|^include" | linesToRa /dev/stdin /dev/stdout | sed 's?searchTrix ?& /gbdb/chm13/?' | sed 's?bigDataUrl ?& /gbdb/chm13/?' > trackDb.ra
 
-wget "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.userTrackDb.txt" -O - | sed 's?bigDataUrl ?& /gbdb/chm13/?'  >> trackDb.ra
+wget "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.userTrackDb.txt" -O - | sed 's?searchTrix ?& /gbdb/chm13/?' | sed 's?bigDataUrl ?& /gbdb/chm13/?'  >> trackDb.ra
 
 mkdir html
 cp /usr/local/apache/htdocs-hgdownload/hubs/GCA/009/914/755/GCA_009914755.4/html/* html
 
 hgsql -Ne "create database chm13"
 cd  ~/kent/src/hg/makeDb/trackDb
 make DBS=chm13
+# had to fix following errors
+# Duplicate tag shortLabel in record starting line 817 of /cluster/home/braney/kent/src/hg/makeDb/trackDb/human/chm13/trackDb.ra
+
+
 # hgTrackDb doesn't find html if the trackDb has already appended the .html
 # hgTrackDb barfs on dollar signs because it assumes it's a variable (windowmasker, hgLiftOver)
 # Track chm13.T2T_Encode has non-conforming 'cell' tag '22Rv1' (begins with digit)
 # multiple shortLabel lines