ac27d7813d12d6ab32beb763204e6fb4dc8ad538
chmalee
  Tue Jan 18 10:21:48 2022 -0800
Fix path bug in clinGen gene-disease validity build script, refs Lou email

diff --git src/hg/utils/otto/clinGen/makeGeneValidity.sh src/hg/utils/otto/clinGen/makeGeneValidity.sh
index 84ddb6e..5d8318d 100755
--- src/hg/utils/otto/clinGen/makeGeneValidity.sh
+++ src/hg/utils/otto/clinGen/makeGeneValidity.sh
@@ -27,22 +27,22 @@
 
 # connect and list a directory, result to file: ls.check
 ftp -n -v -i ftp.clinicalgenome.org 2>&1 < ftp.geneDiseaseValidity.cmds &> ls.check
 grep "hg.*ClinGenBigBed.bb" ls.check | sort > release.list || echo "Error - no bigBed files found"
 
 # see if anything is changing, if so, notify, download, and build
 diff prev.release.list release.list > release.diff || true
 count=`wc -l release.diff | cut -d' ' -f1`
 if [ "${count}" -gt 1 ]; then
     printf "New ClinGen Gene-Disease tracks\n"
     today=`date +%F`
     mkdir -p $today
     cd $today
     wget -N -q "ftp://ftp.clinicalgenome.org/hg19ClinGenBigBed.bb"
     wget -N -q "ftp://ftp.clinicalgenome.org/hg38ClinGenBigBed.bb"
-    cp ClinGenHub/hg19/hg19ClinGenBigBed.bb ${WORKDIR}/release/hg19/clinGenGeneDisease.bb
-    cp ClinGenHub/hg38/hg38ClinGenBigBed.bb ${WORKDIR}/release/hg38/clinGenGeneDisease.bb
+    cp hg19ClinGenBigBed.bb ${WORKDIR}/release/hg19/clinGenGeneDisease.bb
+    cp hg38ClinGenBigBed.bb ${WORKDIR}/release/hg38/clinGenGeneDisease.bb
     cd ..
     echo "ClinGen Gene-Disease update done: `date`"
 else
     echo "No update"
 fi