e965f818e4a97df1b61a718e80cd56054eb628e6
braney
  Fri Sep 21 12:51:22 2012 -0700
move decipher directory to be level with omim directory. (#8840)
diff --git src/utils/decipher/checkDecipher.sh src/utils/decipher/checkDecipher.sh
deleted file mode 100755
index 729c1f8..0000000
--- src/utils/decipher/checkDecipher.sh
+++ /dev/null
@@ -1,93 +0,0 @@
-#!/bin/sh -ex
-
-#	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 $HOME/bin/scripts/
-
-#	cron jobs need to ensure this is true
-umask 002
-
-WORKDIR="/hive/data/outside/otto/decipher"
-export WORKDIR
-
-#	this is where we are going to work
-if [ ! -d "${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`
-
-#	create ftp response script for the ftp connection session
-rm -f ftp.decipher.rsp
-echo "user ftp-decipher-dda ${ftppass}
-cd pub
-ls
-bye" > ftp.decipher.rsp
-
-#	reorganize results files
-rm -f prev.release.list
-rm -f ls.check
-cp -p release.list prev.release.list
-rm -f release.list
-
-#	connect and list a directory, result to file: ls.check
-ftp -n -v -i ftp.sanger.ac.uk  < ftp.decipher.rsp > ls.check
-
-#	fetch the release directory names from the ls.check result file
-grep "decipher-hg19" ls.check | sort > release.list
-chmod o+w release.list
-
-#	verify we are getting a proper list
-WC=`cat release.list | wc -l`
-if [ "${WC}" -lt 1 ]; then
-    echo "potential error in DECIPHER release watch,
-check release.list in ${WORKDIR}" 
-    exit 255
-fi
-
-#	see if anything is changing, if so, email notify, download, and build
-
-diff prev.release.list release.list  >release.diff || true
-WC=`cat release.diff | wc -l`
-if [ "${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`"/" 
-
-
-    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
-