710f5b14245de8fc6cdf47e281f7f83178ab5205
braney
  Thu Sep 20 08:55:56 2012 -0700
checking in the scripts that Fan was actually using to update decipher (#8840)
diff --git src/utils/decipher/checkDecipher.sh src/utils/decipher/checkDecipher.sh
index 18b6a44..1187b3a 100755
--- src/utils/decipher/checkDecipher.sh
+++ src/utils/decipher/checkDecipher.sh
@@ -1,99 +1,99 @@
 #!/bin/sh
 
 #	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/
 
 # set EMAIL here for notification list
 EMAIL="fanhsu@soe.ucsc.edu"
 # set DEBUG_EMAIL here for notification of potential errors in the process
 DEBUG_EMAIL="fanhsu@soe.ucsc.edu"
 
 #	cron jobs need to ensure this is true
 umask 002
 
 WORKDIR="/hive/groups/gsid/medical/fan/decipher/auto"
 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}" \
 	| mail -s "ERROR: DECIPHER watch" ${DEBUG_EMAIL}
     exit 255
 fi
 
 cd "${WORKDIR}"
 
 ftppass=`cat ftp.pwd`
 gpgpass=`cat gpg.pwd`
 
 #	create ftp response script for the ftp connection session
 rm -f ftp.decipher.rsp
 echo "user ftp-decipher-dda ${ftppass}
 cd pub
 ls
 bye" > ftp.decipher.rsp
 
 #	reorganize results files
 rm -f prev.release.list
 rm -f ls.check
 cp -p release.list prev.release.list
 rm -f release.list
 
 #	connect and list a directory, result to file: ls.check
 ftp -n -v -i ftp.sanger.ac.uk  < ftp.decipher.rsp > ls.check
 
 #	fetch the release directory names from the ls.check result file
 grep "decipher-" ls.check | sort > release.list
 chmod o+w release.list
 
 #	verify we are getting a proper list
 WC=`cat release.list | wc -l`
 if [ "${WC}" -lt 1 ]; then
     echo "potential error in DECIPHER release watch,
 check release.list in ${WORKDIR}" \
 	| mail -s "ERROR: DECIPHER watch" ${DEBUG_EMAIL}
     exit 255
 fi
 
 #	see if anything is changing, if so, email notify, download, and build
 
 diff prev.release.list release.list  >release.diff
 WC=`cat release.diff | wc -l`
 if [ "${WC}" -gt 1 ]; then
     echo -e "New DECIPHER update noted at:\n" \
 "ftp://ftp.sanger.ac.uk/pub/\n"`comm -13 prev.release.list release.list`"/" \
     | mail -s "DECIPHER update watch" ${EMAIL}
 
-FN=`cat release.diff |grep decipher-|sed -e 's/decipher-/\tdecipher-/'|cut -f 2`
+FN=`cat release.diff |grep decipher-|sed -e 's/decipher-/\tdecipher-/'|cut -f 2|tail -1`
 
 today=`date +%F`
 mkdir -p $today
 cd $today
-
+cp -p ../*.diff .
 echo "${FN}" >j.fn.gpg
 cat j.fn.gpg |sed -e 's/.gpg//' >j.fn.txt
 
 # prepare ftp download response file
 rm -f ftp.decipher.rsp
 echo "user ftp-decipher-dda ${ftppass}
 cd pub
 get "${FN}"
 bye" > ftp.decipher.rsp
 
 # download the new data file
 ftp -n -v -i ftp.sanger.ac.uk  < ftp.decipher.rsp > ftp.log
 
 #rm -f `cat j.fn.txt`
 
 # unpack the gpg encrypted file
 gpg --passphrase "${gpgpass}"  "${FN}"
 
 # build the new DECIPHER track tables
 ../buildDecipher `cat j.fn.txt`
 
 rm j.fn.txt
 rm j.fn.gpg
 fi