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
@@ -1,48 +1,48 @@
 #!/bin/bash
 
 # downloads and builds the ClinGen Gene Validity track
 # assumes running in the build directory:
 # /hive/data/outside/otto/clinGen/
 set -beEu -o pipefail
 
 WORKDIR=$1
 mkdir -p ${WORKDIR}/clinGenGeneValidity
 cd ${WORKDIR}/clinGenGeneValidity
 
 # the release directory, where gbdb symlinks will point
 if [ ! -d release ]; then
     mkdir -p ${WORKDIR}/release/{hg19,hg38}
 fi
 
 echo "user anonymous
 ls hg*ClinGenBigBed.bb
 bye" > ftp.geneDiseaseValidity.cmds
 
 if [ -e release.list ]
 then
     mv release.list prev.release.list
 fi
 touch prev.release.list
 rm -f release.list
 
 # 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