ee617db835fea5844d9fbf28559f3bb515ef75ae
jnavarr5
  Mon Oct 27 15:24:18 2025 -0700
Unzipping the contents of the gwas catalog before continuing with the script, no Redmine

diff --git src/hg/utils/otto/gwas/checkGwas.sh src/hg/utils/otto/gwas/checkGwas.sh
index e2ac325fd03..02a93d909c8 100755
--- src/hg/utils/otto/gwas/checkGwas.sh
+++ src/hg/utils/otto/gwas/checkGwas.sh
@@ -13,31 +13,32 @@
 umask 002
 
 WORKDIR=$1
 export WORKDIR
 export PATH=$WORKDIR":$PATH"
 
 #	this is where we are going to work
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in GWAS release watch, Can not find the directory:     ${WORKDIR}" 
     exit 255
 fi
 
 cd "${WORKDIR}"
 
 # Note: timestamping no longer works
-wget -q --timestamping  -O gwascatalog.txt https://www.ebi.ac.uk/gwas/api/search/downloads/associations/v1.0?split=false
+wget -q --timestamping -O gwascatalog.zip https://www.ebi.ac.uk/gwas/api/search/downloads/associations/v1.0?split=false
+unzip -p gwascatalog.zip > gwascatalog.txt; rm gwascatalog.zip
 if [  ! gwascatalog.txt  -nt old.gwascatalog.txt ]; then
     echo "Not newer"
     exit 0
 fi
 
 today=`date +%y%m%d`
 mkdir $today
 cp gwascatalog.txt $today
 mv gwascatalog.txt old.gwascatalog.txt
 
 cd $today
 
 head -1 gwascatalog.txt | sed -re 's/\t/\n/g' | tr -d '\r' > foundColumns.txt
 
 if cmp foundColumns.txt ../expectedColumns.txt