76e480f51fbf36171248a26c9f24c3bd0e95af7f
kate
  Thu Jun 4 11:38:18 2020 -0700
Save build script and schema for CCRE track. refs #24668

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 819c8e3..a12e314 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -17815,23 +17815,25 @@
 wget -nd https://users.wenglab.org/moorej3/mouse-maxz-dnase.txt.gz
 gunzip Mouse-maxZ-DNase.txt.gz
 
 sort Mouse-maxZ-DNase.txt > Mouse-maxZ-DNase.sorted.txt
 # noting that order of accessions in score file doesn't match bed file ;-(
 sort -k 4 mm10-ccREs.bed > mm10-ccREs.sorted.bed
 paste mm10-ccREs.sorted.bed Mouse-maxZ-DNase.sorted.txt > ccres.prescored.bed
 # sanity check ids match
 
 # score using zscore,  min(zscore*100),1000), and reformat
 awk '{OFS="\t"; print $1, $2, $3, $4, ($13>10)? 1000 : int($13 * 100), $6, $7, $8, $9, $10, $13}' \
         ccres.prescored.bed | bedSort stdin ccres.scored.bed
 set f = encodeCcreCombined
 
 # Reformat to add fields for filtering and mouseover, etc.
-perl ../makeCcreCombined.pl < ccres.scored.bed > $f.bed
-bedToBigBed -tab -type=bed9+6 -as=../$f.as $f.bed /hive/data/genomes/mm10/chrom.sizes $f.bb
+set bin = ~/kent/src/hg/makeDb/outside/encode3/ccre
+perl $bin/makeCcreCombined.pl < ccres.scored.bed > $f.bed
+set lib = ~/kent/src/hg/lib
+bedToBigBed -tab -type=bed9+6 -as=$lib/$f.as $f.bed /hive/data/genomes/mm10/chrom.sizes $f.bb
 mkdir -p /gbdb/mm10/encode3/ccre
 ln -s `pwd`/$f.bb /gbdb/mm10/encode3/ccre
 
 
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