d6d6967d21a36badceed77f26525ec10c8540ebf
jcasper
  Tue Apr 5 17:40:55 2022 -0700
Updates to the DECIPHER pipeline, first for a manual build, refs #29130

diff --git src/hg/utils/otto/decipher/checkDecipher.sh src/hg/utils/otto/decipher/checkDecipher.sh
index cf3f945..6496a2a 100755
--- src/hg/utils/otto/decipher/checkDecipher.sh
+++ src/hg/utils/otto/decipher/checkDecipher.sh
@@ -1,80 +1,82 @@
 #!/bin/sh -e
 set -eEu -o pipefail
 #	Do not modify this script, modify the source tree copy:
 #	src/utils/decipher/checkDecipher.sh
 #	This script is used via a cron job and kept in $HOME/bin/scripts/
 
 #	cron jobs need to ensure this is true
 #       current login requires the user be braney
 umask 002
 
 trap reportErr ERR
 
 function reportErr
 {
     echo "ERROR: DECIPHER pipeline failed"
     exit 1;
 }
 
 
 WORKDIR="/hive/data/outside/otto/decipher"
 export WORKDIR
 
 #	this is where we are going to work
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in DECIPHER release watch, Can not find the directory:
     ${WORKDIR}" 
     exit 255
 fi
 
 cd "${WORKDIR}"
 
 #ftppass=`cat ftp.pwd`
 #gpgpass=`cat gpg.pwd`
 
 perl login.perl > /dev/null 2>&1
 
 if test decipher-variants*.gpg -nt lastUpdate
 then
     today=`date +%F`
     mkdir -p $today
 
     CNV=decipher-cnvs*.gpg
     SNV=decipher-snvs*.gpg
     cp -p $CNV $SNV $today
 
     cd $today
 
     # unpack the gpg encrypted file
     gpg --batch --passphrase-file "../gpg.pwd.new" ${CNV}
     gpg --batch --passphrase-file "../gpg.pwd.new" ${SNV}
 
     mkdir -p ${WORKDIR}/release/{hg38,hg19}
 
     # build the new DECIPHER track tables (builds bigBed for cnv's)
+    # THIS NEEDS TO CHANGE - NEW ARGUMENT IS JUST ONE VARIANT FILE FROM DECIPHER,
+    # BUT FIRST WE'LL NEED TO FIX THE FETCH SCRIPT
     ../buildDecipher `basename $CNV .gpg` `basename $SNV .gpg`
     ../validateDecipher.sh hg38
     #../validateDecipher.sh hg19
 
     # now install
     #for db in hg38 hg19
     for db in hg38
     do
         for i in `cat ../decipher.tables`
         do 
         n=$i"New"
         o=$i"Old"
         hgsqlSwapTables $db $n $i $o -dropTable3
         done
     done
 
     echo "DECIPHER Installed `date`" 
 
     # Variants BED will be updated for both CNV and SNV updates
     cd ${WORKDIR}
     cp -p decipher-var*.gpg lastUpdate
 else
     echo "No update"
 fi
 
 rm decipher-*