diff --git a/Configuration.default b/Configuration.default
index f7f74fd..e82c16f 100644
--- a/Configuration.default
+++ b/Configuration.default
@@ -1,71 +1,109 @@
-#!/bin/csh
+#!/bin/sh
 
 #
 # Configuration.default
 #
-# Source this file from any csh script to set the env variables
+# Source this file from any bourne shell script to set the
+# env variables
 #
+#
+#  If the MGICONFIG environment variable does not have a local override,
+#  use the default "live" settings.
+#
+if [ "${MGICONFIG}" = "" ]
+then
+    MGICONFIG=/usr/local/mgi/live/mgiconfig
+    export MGICONFIG
+fi
 
-if ( ${?MGICONFIG} == 0 ) then
-	setenv MGICONFIG /usr/local/mgi/live/mgiconfig
-endif
-
-source ${MGICONFIG}/master.config.csh
+. ${MGICONFIG}/master.config.sh
 
 # install directory
-setenv CACHEINSTALLDIR		${DBUTILS}/snpcacheload
+CACHEINSTALLDIR=${DBUTILS}/snpcacheload
 
 # output dir
-setenv CACHEDIR 		/data/loads/mgi/snpcacheload
+CACHEDIR=/data/loads/mgi/snpcacheload
 
 # data directory
-setenv CACHEDATADIR             ${CACHEDIR}/output
+CACHEDATADIR=${CACHEDIR}/output
 
 # logs directory
-setenv CACHELOGSDIR             ${CACHEDIR}/logs
+CACHELOGSDIR=${CACHEDIR}/logs
 
-# full path to back-end snp database backup file. 
-# this directory is on the unix server on which the sybase server resides
-# e.g. lindon when backing up PROD1_MGI..snp
-setenv SNP_BACKUP	/extra1/sybase/snp.backup
+# directory in which to archive the contents of output and logs directories
+ARCHIVEDIR=${CACHEDIR}/archive
 
-# full path to SNP_BACKUP in order to load it from shire (weekly snpcacheload)
-setenv PRODSNP_BACKUP   /net/mtdoom/vol/lindon${SNP_BACKUP}
+export CACHEINSTALLDIR CACHEDIR CACHEDATADIR CACHELOGSDIR ARCHIVEDIR
+
+#
+# settings for snpmarker_weekly.sh 
+#
+# full path to PROD1_MGI..snp backup file on lindon
+SNP_BACKUP_LOCALPATH=/extra1/sybase/snp.backup
+
+export SNP_BACKUP_LOCALPATH
+
+# source this for file archiving and other utilities
+DLAJOBSTREAMFUNC=${DBUTILS}/dlautils/DLAJobStreamFunctions.sh
+
+export DLAJOBSTREAMFUNC
 
 # mgd refseq _LogicalDB_key
-setenv REFSEQ_LOGICALDB_KEY     27
+REFSEQ_LOGICALDB_KEY=27
 
 # mgd SNP_ConsensusSnp_Marker _MGIType_key
-setenv SNPMRKR_MGITYPE_KEY              32
+SNPMRKR_MGITYPE_KEY=32
 
 # mgd refSNP _LogicalDB_key
-setenv CS_LOGICALDB_KEY         73
+CS_LOGICALDB_KEY=73
 
 # mgd SNP_ConsensusSnp _LogicalDB_key
-setenv CS_MGITYPE_KEY           30
+CS_MGITYPE_KEY=30
+
+export REFSEQ_LOGICALDB_KEY SNPMRKR_MGITYPE_KEY CS_LOGICALDB_KEY CS_MGITYPE_KEY
 
 # mgd EntrezGene _LogicalDB_key
-setenv EG_LOGICALDB_KEY         55
+EG_LOGICALDB_KEY=55
 
 # mgd MRK_Marker _MGIType_key
-setenv MRKR_MGITYPE_KEY 2
+MRKR_MGITYPE_KEY=2
+
+# QTL MRK_Marker _Marker_Type_key
+MRKR_QTLTYPE_KEY=6
+
+export EG_LOGICALDB_KEY MRKR_MGITYPE_KEY MRKR_QTLTYPE_KEY
 
 # snp table and bcp file names 
-setenv ACC_TABLE	SNP_Accession
-setenv ACC_FILE		${ACC_TABLE}.bcp
-setenv TMP_FXN_TABLE	TMP_SNP_Marker_Fxn
-setenv TMP_FXN_FILE	${TMP_FXN_TABLE}.bcp
-setenv SNP_MRK_TABLE	SNP_ConsensusSnp_Marker
-setenv SNP_MRK_FILE	${SNP_MRK_TABLE}.bcp
-setenv SNP_MRK_WITHIN_FILE	${SNP_MRK_TABLE}_Within.bcp
-setenv MRKLOC_CACHETABLE	MRK_Location_Cache
-setenv MRKLOC_CACHEFILE	${MRKLOC_CACHETABLE}.bcp
+ACC_TABLE=SNP_Accession
+ACC_FILE=${ACC_TABLE}.bcp
+
+export ACC_TABLE ACC_FILE
+
+TMP_FXN_TABLE=TMP_SNP_Marker_Fxn
+TMP_FXN_FILE=${TMP_FXN_TABLE}.bcp
+
+export TMP_FXN_TABLE TMP_FXN_FILE
+
+SNP_MRK_TABLE=SNP_ConsensusSnp_Marker
+SNP_MRK_FILE=${SNP_MRK_TABLE}.bcp
+SNP_MRK_WITHIN_FILE=${SNP_MRK_TABLE}_Within.bcp
+
+export SNP_MRK_TABLE SNP_MRK_FILE SNP_MRK_WITHIN_FILE
+
+MRKLOC_CACHETABLE=MRK_Location_Cache
+MRKLOC_CACHEFILE=${MRKLOC_CACHETABLE}.bcp
+
+export MRKLOC_CACHETABLE MRKLOC_CACHEFILE
 
 # max number of lines per bcp file to keep below 2G
-setenv MAX_BCP_LINES	25000000 
+MAX_BCP_LINES=25000000 
 
 # max number of ConsensusSnp keys in a snpmrkwithin.py query batch
-setenv MAX_QUERY_BATCH  100000
+MAX_QUERY_BATCH=100000
+
+export MAX_BCP_LINES MAX_QUERY_BATCH
 
 # Are dbSNP and MGI coordinates synchronized (same mouse genome build) ?
-setenv IN_SYNC	yes
+IN_SYNC=yes
+
+export IN_SYNC
diff --git a/HISTORY b/HISTORY
index 64e06e7..ab89d40 100644
--- a/HISTORY
+++ b/HISTORY
@@ -1,3 +1,47 @@
+TAG: snpcacheload-3-5-1-1
+DATE: 09/06/2006
+STAFF: sc
+RELEASE: MGI3.51, build 36
+CHANGES: merge build36 branch to trunK (note this is a second merge
+         of this branch to the trunk
+
+TAG: snpcacheload-mgiconfig-7
+DATE: 09/06/2006
+STAFF: sc
+RELEASE: MGI3.51, build 36
+CHANGES:
+1) added system_docs
+
+TAG: snpcacheload-mgiconfig-6
+TAG: snpcacheload-mgiconfig-5
+DATE: 08/24/2006
+STAFF: sc
+RELEASE: MGI3.51, build 36
+CHANGES:
+1) corrected mgidbutilities config var name
+2) added sys.stdout.flush
+
+TAG: snpcacheload-mgiconfig-4
+DATE: 08/10/2006
+STAFF: sc
+RELEASE: MGI3.51, build 36
+CHANGES:
+1) remove snplocation.py
+2) Configuration - removed SNP_BACKUP_REMOTEPATH to mgiconfig
+                 - updated SNP_BACKUP to SNP_BACKUP_LOCALPATH
+		 - added MRKR_QTLTYPE_KEY
+3) snpmarker_weekly.sh - updated to use SNP_BACKUP_REMOTEPATH and 
+                 SNP_BACKUP_LOCALPATH
+4) snpmrkwithin.py - updated to not load distance relationships, only
+                   - update locus_region and determine 'within coordinates of'
+
+TAG: snpcacheload-mgiconfig-3
+DATE: 08/01/2006
+STAFF: sc
+RELEASE: MGI3.51, build 36
+CHANGES:
+1) converted to bourne shell
+
 TAG: snpcacheload-3-5-0-4
 DATE: 07/01/2006
 STAFF: lec
diff --git a/Install b/Install
index 412d688..d24b47c 100755
--- a/Install
+++ b/Install
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/sh
 
 #
 # Install
@@ -9,19 +9,26 @@
 # 2. ln -s snpcacheload-#-#-# snpcacheload
 # 3. Copy Configuration.default Configuration
 # 4. Edit Configuration
-#
+# 5. Install
 
-cd `dirname $0` && source ./Configuration
+cd `dirname $0` && . ./Configuration
 
-if ( ! -d ${CACHEDIR} ) then
+if [ ! -d ${CACHEDIR} ]
+then
         mkdir -p ${CACHEDIR}
-endif
+fi
 
-if ( ! -d ${CACHEDATADIR} ) then
+if [ ! -d ${CACHEDATADIR} ] 
+then
         mkdir -p ${CACHEDATADIR}
-endif
+fi
 
-if ( ! -d ${CACHELOGSDIR} ) then
+if [ ! -d ${CACHELOGSDIR} ] 
+then
         mkdir -p ${CACHELOGSDIR}
-endif
+fi
 
+if [ ! -d ${ARCHIVEDIR} ] 
+then
+        mkdir -p ${ARCHIVEDIR}
+fi
diff --git a/snpmarker.py b/snpmarker.py
index 58611e8..f559a34 100755
--- a/snpmarker.py
+++ b/snpmarker.py
@@ -16,9 +16,11 @@
 #    	   2) bcp files
 # History
 #
-# 08/17/2005	sc
-#	- SNP (TR 1560)
-# 03/16/2006 sc convert to snp database
+# lec   06/30/2006 - modified for mgiconfig
+#
+# sc	03/16/2006 - convert to snp database
+#
+# sc    08/17/2005 - SNP (TR 1560)
 #
 # lec   06/30/2006 - modified for mgiconfig
 #
@@ -89,6 +91,7 @@ def initialize():
     # Effects: queries a database
     # Throws:  db.error, db.connection_exc
     print 'connecting to mgd and loading markerLookup...%s' % NL
+    sys.stdout.flush()
     # set up connection to the mgd database
     db.useOneConnection(1)
     db.set_sqlLogin(user, password, mgdServer, mgdDB)
@@ -108,8 +111,10 @@ def initialize():
 	markerLookup[ r['egId'] ] = r['_Marker_key'] 
     
     print 'connecting to %s..%s ...%s' % (snpServer, snpDB, NL)
+    sys.stdout.flush()
     # set up connection the snp database
     db.useOneConnection(0)
+    db.useOneConnection(1)
     db.set_sqlLogin(user, password, snpServer, snpDB)
 
 def deleteAccessions():
@@ -119,6 +124,7 @@ def deleteAccessions():
     # Effects: queries a database, deletes records from a database
     # Throws:  db.error, db.connection_exc
     print 'deleting accessions ...%s' % NL
+    sys.stdout.flush()
 
     cmds = []
     cmds.append('select a._Accession_key ' + \
@@ -145,6 +151,7 @@ def getMaxAccessionKey():
     # current max(_Accession_key)
     global accKey
     print 'getting max snp accession key ...%s' % NL
+    sys.stdout.flush()
     cmds = []
     cmds.append('select max(_Accession_key) ' + \
             'from SNP_Accession')
@@ -162,6 +169,7 @@ def createBCP():
     print 'creating %s...%s' % (snpMrkrFile, mgi_utils.date())
     print 'and  %s...%s%s' % (accFile, mgi_utils.date(), NL)
     print 'querying ... %s' % NL
+    sys.stdout.flush()
 
     cmds = []
     # get set of DP_SNP_Marker attributes into a temp table
@@ -186,6 +194,7 @@ def createBCP():
     results = db.sql(cmds, 'auto')
     
     print 'writing bcp file ...%s' % NL
+    sys.stdout.flush()
     # current primary key
     primaryKey = 0
     for r in results[1]:
@@ -272,6 +281,7 @@ def finalize():
 #
 
 print 'snpmarker.py start: %s' % mgi_utils.date()
+sys.stdout.flush()
 try:
     initialize()
     getMaxAccessionKey()
@@ -288,4 +298,5 @@ def finalize():
     sys.exit(message)
 
 print 'snpmarker.py end: %s' % mgi_utils.date()
+sys.stdout.flush()
 
diff --git a/snpmarker.sh b/snpmarker.sh
new file mode 100755
index 0000000..b58be9e
--- /dev/null
+++ b/snpmarker.sh
@@ -0,0 +1,357 @@
+#!/bin/sh 
+
+#
+# Program: snpmarker.sh
+#
+# Purpose:
+#
+#       Script for loading SNP_ConsensusSnp_Marker table
+#       with dbSNP determined snp to marker associations
+#       and MGI determined snp to marker associations.
+#
+# Usage:  snpmarker.sh [-a] [-r] [-c] [-l] 
+#         where: 
+#             -a is an option to archive output directory
+#             -r is an option to archive logs directory	
+#             -c is an option to clean output directory
+#             -l is an option to clean logs directory
+#
+# History
+#
+# sc    07/27/2006 - converted to bourne shell
+# lec   06/30/2006 - modified for mgiconfig
+# sc    03/2006 - convert to snp database add load of snp MRK_Location_Cache
+# sc    01/2006 - process multiple snpmrkwithin.bcp files
+# dbm   09/28/2005 - Added snpmrklocus.py & snpmrkwithin.py
+# sc	08/17/2005 - created
+
+#
+# Establish bcp file delimiters
+# 
+
+# bcp file row delimiter
+NL="\n"
+
+# bcp file column delimiter
+DL="|"
+
+#
+#  Set up a log file for the shell script in case there is an error
+#  during configuration and initialization.
+#
+cd `dirname $0` 
+LOG=`pwd`/snpmarker.log
+rm -f ${LOG}
+
+#
+#  Verify the argument(s) to the shell script.
+#
+ARC_OUTPUT=no
+ARC_LOGS=no
+CLEAN_OUTPUT=no
+CLEAN_LOGS=no
+
+usage="Usage: snpmarker.sh [-a] [-r] [-c] [-l]"
+#
+# report usage if there are unrecognized arguments
+#
+set -- `getopt arcl $*`
+if [ $? != 0 ]
+then
+    echo ${usage} | tee -a ${LOG}
+    exit 1
+fi
+
+#
+# determine which options on command line
+#
+for i in $*
+do
+    case $i in
+        -a) ARC_OUTPUT=yes; shift;;
+        -r) ARC_LOGS=yes; shift;;
+	-c) CLEAN_OUTPUT=yes; shift;;
+	-l) CLEAN_LOGS=yes; shift;;
+        --) shift; break;;
+    esac
+done
+
+#
+#  Establish the configuration file name, if readable source it
+#
+CONFIG_LOAD=`pwd`/Configuration
+if [ ! -r ${CONFIG_LOAD} ]
+then
+    echo "Cannot read configuration file: ${CONFIG_LOAD}" | tee -a ${LOG}
+    exit 1
+fi
+
+. ${CONFIG_LOAD}
+
+#
+#  Source the DLA library functions.
+#
+if [ "${DLAJOBSTREAMFUNC}" != "" ]
+then
+    if [ -r ${DLAJOBSTREAMFUNC} ]
+    then
+        . ${DLAJOBSTREAMFUNC}
+    else
+        echo "Cannot source DLA functions script: ${DLAJOBSTREAMFUNC}" | tee -a ${LOG}
+        exit 1
+    fi
+else
+    echo "Environment variable DLAJOBSTREAMFUNC has not been defined." | tee -a ${LOG}
+    exit 1
+fi
+
+# 
+# archive/clean the logs/output directories?
+#
+if [ ${ARC_OUTPUT} = "yes" ]
+then
+    date | tee -a ${LOG}
+    echo "archiving  output directory" | tee -a ${LOG}
+    createArchive ${ARCHIVEDIR}/output ${CACHEDATADIR}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "createArchive for output directory failed" | tee -a ${LOG}
+        exit 1
+    fi
+fi
+
+if [ ${CLEAN_OUTPUT} = "yes" ]
+then
+    date | tee -a ${LOG}
+    echo "cleaning  output directory" | tee -a ${LOG}
+    cleanDir ${CACHEDATADIR}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "cleanDir for output directory failed" | tee -a ${LOG}
+        exit 1
+    fi
+
+fi
+
+if [ ${ARC_LOGS} = "yes" ]
+then
+    date | tee -a ${LOG}
+    echo "archiving logs directory" | tee -a ${LOG}
+    createArchive ${ARCHIVEDIR}/logs ${CACHELOGSDIR}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "createArchive for logs directory failed" | tee -a ${LOG}
+        exit 1
+    fi
+fi
+
+if [ ${CLEAN_LOGS} = "yes" ]
+then
+    date | tee -a ${LOG}
+    echo "cleaning logs directory" | tee -a ${LOG}
+    cleanDir ${CACHELOGSDIR}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "cleanDir for logs directory failed" | tee -a ${LOG}
+        exit 1
+    fi
+fi
+
+date | tee -a ${LOG}
+
+#
+#   Establish the load log now that we have archived/cleaned
+#
+LOAD_LOG=${CACHELOGSDIR}/`basename $0`.log
+date | tee -a ${LOAD_LOG}
+
+cd ${CACHEDATADIR}
+
+#
+# Allow bcp into database
+#
+date | tee -a ${LOAD_LOG}
+echo "Allow bcp into database" | tee -a ${LOAD_LOG}
+${MGI_DBUTILS}/bin/turnonbulkcopy.csh ${SNPBE_DBSERVER} ${SNPBE_DBNAME} | tee -a ${LOAD_LOG}
+
+#
+# Load dbSNP marker relationships
+#
+
+# create bcp file
+echo "Calling snpmarker.py" | tee -a ${LOAD_LOG}
+${CACHEINSTALLDIR}/snpmarker.py | tee -a ${LOAD_LOG}
+STAT=$?
+if [ ${STAT} -ne 0 ]
+then
+    echo "snpmarker.py failed" | tee -a ${LOAD_LOG}
+    exit 1
+fi
+
+# SNP_MRK_TABLE truncate, drop indexes, bcp in, create indexes
+date | tee -a ${LOAD_LOG}
+echo "bcp in  ${SNP_MRK_TABLE}" | tee -a ${LOAD_LOG}
+echo "" | tee -a ${LOAD_LOG}
+${MGI_DBUTILS}/bin/bcpin_withTruncateDropIndex.csh ${SNPBE_DBSCHEMADIR} ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${SNP_MRK_TABLE} ${CACHEDATADIR} ${SNP_MRK_FILE} ${DL} ${NL}
+STAT=$?
+if [ ${STAT} -ne 0 ]
+then
+    echo "${MGI_DBUTILS}/bin/bcpin_withTruncateDropIndex.csh failed" | tee -a ${LOAD_LOG}
+    exit 1
+fi
+
+# SNP_MRK_TABLE update statistics
+echo "" | tee -a ${LOAD_LOG}
+date | tee -a ${LOAD_LOG}
+echo "Update statistics on ${SNP_MRK_TABLE} table" | tee -a ${LOAD_LOG}
+${MGI_DBUTILS}/bin/updateStatistics.csh ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${SNP_MRK_TABLE} | tee -a ${LOAD_LOG}
+
+#
+# bcp in ACC_TABLE, dropping/recreating indexes
+#
+
+# ACC_TABLE drop indexes
+echo "" | tee -a ${LOG}
+date | tee -a ${LOG}
+echo "Drop indexes on ${ACC_TABLE} table" | tee -a ${LOG}
+${SNPBE_DBSCHEMADIR}/index/${ACC_TABLE}_drop.object | tee -a ${LOG}
+
+# ACC_TABLE bcp in
+date | tee -a ${LOAD_LOG}
+echo "bcp in  ${ACC_TABLE} " | tee -a ${LOAD_LOG}
+echo "" | tee -a ${LOAD_LOG}
+${MGI_DBUTILS}/bin/bcpin.csh ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${ACC_TABLE} ${CACHEDATADIR} ${ACC_FILE} ${DL} ${NL}
+STAT=$?
+if [ ${STAT} -ne 0 ]
+then
+    echo "${MGI_DBUTILS}/bin/bcpin.csh failed" | tee -a ${LOAD_LOG}
+    exit 1
+fi
+
+# ACC_TABLE create indexes
+echo "" | tee -a ${LOG}
+date | tee -a ${LOG}
+echo "Create indexes on ${ACC_TABLE} table" | tee -a ${LOG}
+${SNPBE_DBSCHEMADIR}/index/${ACC_TABLE}_create.object | tee -a ${LOG}
+
+# ACC_TABLE update statistics
+echo "" | tee -a ${LOAD_LOG}
+date | tee -a ${LOAD_LOG}
+echo "Update statistics on ${ACC_TABLE} table" | tee -a ${LOAD_LOG}
+${MGI_DBUTILS}/bin/updateStatistics.csh ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${ACC_TABLE} | tee -a ${LOAD_LOG}
+
+#
+# Load MGI snp/marker distance relationships
+#
+# Only run the following steps if the dbSNP and MGI coordinates are
+# synchronized (same mouse genome build).
+#
+if [ ${IN_SYNC} = "yes" ] 
+then
+
+    # 
+    # load snp..MRK_Location_Cache
+    #
+
+    # bcp out MRKLOC_CACHETABLE	 
+    echo "" | tee -a ${LOAD_LOG}
+    date | tee -a ${LOAD_LOG}
+    echo "bcp out ${MRKLOC_CACHETABLE}" | tee -a ${LOAD_LOG}
+    ${MGI_DBUTILS}/bin/bcpout.csh ${MGD_DBSERVER} ${MGD_DBNAME} ${MRKLOC_CACHETABLE} ${CACHEDATADIR} ${MRKLOC_CACHEFILE} ${DL} ${NL} | tee -a ${LOAD_LOG}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+	echo "${MGI_DBUTILS}/bin/bcpout.csh failed" | tee -a ${LOAD_LOG}
+	exit 1
+    fi
+
+    # bcp in MRKLOC_CACHETABLE, truncating and dropping/recreating indexes
+    echo "" | tee -a ${LOAD_LOG}
+    date | tee -a ${LOAD_LOG}
+    echo "bcp in MRK_Location_Cache" | tee -a ${LOAD_LOG}
+    ${MGI_DBUTILS}/bin/bcpin_withTruncateDropIndex.csh ${SNPBE_DBSCHEMADIR} ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${MRKLOC_CACHETABLE} ${CACHEDATADIR} ${MRKLOC_CACHEFILE} ${DL} ${NL}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "${MGI_DBUTILS}/bin/bcpin_withTruncatDropIndex.csh failed" | tee -a ${LOAD_LOG}
+        exit 1
+    fi
+
+    # update statistics
+    echo "updating statistics on ${MRKLOC_CACHETABLE}" | tee -a  ${LOAD_LOG}
+    ${MGI_DBUTILS}/bin/updateStatistics.csh ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${MRKLOC_CACHETABLE} | tee -a ${LOAD_LOG}
+
+    #
+    # Update dbSNP locus-region function class to upstream/downstream
+    #
+
+    echo "" | tee -a ${LOAD_LOG} 
+    date | tee -a ${LOAD_LOG}
+    echo "Calling snpmrklocus.py" | tee -a ${LOAD_LOG}
+    ${CACHEINSTALLDIR}/snpmrklocus.py | tee -a ${LOAD_LOG}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "${CACHEINSTALLDIR}/snpmrklocus.py failed" | tee -a ${LOAD_LOG}
+        exit 1
+    fi
+
+    #
+    # load MGI snp to marker relationships
+    # 
+
+    # create the bcp file(s)
+    echo "" | tee -a ${LOAD_LOG}
+    date | tee -a ${LOAD_LOG}
+    echo "Calling snpmrkwithin.py" | tee -a ${LOAD_LOG}
+    ${CACHEINSTALLDIR}/snpmrkwithin.py | tee -a ${LOAD_LOG}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "${CACHEINSTALLDIR}/snpmrkwithin.py failed" | tee -a ${LOAD_LOG}
+        exit 1
+    fi
+
+    # SNP_MRK_TABLE drop indexes
+    echo "" | tee -a ${LOG}
+    date | tee -a ${LOG}
+    echo "Drop indexes on ${SNP_MRK_TABLE} table" | tee -a ${LOG}
+    ${SNPBE_DBSCHEMADIR}/index/${SNP_MRK_TABLE}_drop.object | tee -a ${LOG}
+    echo "" | tee -a ${LOG}
+
+    # SNP_MRK_TABLE bcp in each file
+    cd ${CACHEDATADIR}
+    for i in `ls ${SNP_MRK_WITHIN_FILE}*`
+    do
+	date | tee -a ${LOAD_LOG}
+	echo "Load ${i} into ${SNP_MRK_TABLE} table" | tee -a ${LOAD_LOG}
+	echo "" | tee -a ${LOAD_LOG}
+	${MGI_DBUTILS}/bin/bcpin.csh ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${SNP_MRK_TABLE} ${CACHEDATADIR} ${i} ${DL} ${NL}
+	STAT=$?
+	if [ ${STAT} -ne 0 ]
+	then
+	    echo "${MGI_DBUTILS}/bin/bcpin.csh failed" | tee -a ${LOAD_LOG}
+	    exit 1
+	fi
+    done
+
+    # SNP_MRK_TABLE create indexes
+    echo "" | tee -a ${LOG}
+    date | tee -a ${LOG}
+    echo "Create indexes on ${SNP_MRK_TABLE} table" | tee -a ${LOG}
+    ${SNPBE_DBSCHEMADIR}/index/${SNP_MRK_TABLE}_create.object | tee -a ${LOG}
+
+    # SNP_MRK_TABLE update statistics
+    echo "" | tee -a ${LOAD_LOG}
+    date | tee -a ${LOAD_LOG}
+    echo "Update statistics on ${SNP_MRK_TABLE} table" | tee -a ${LOAD_LOG}
+    ${MGI_DBUTILS}/bin/updateStatistics.csh ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${SNP_MRK_TABLE} | tee -a ${LOAD_LOG}
+
+fi
+
+echo "" | tee -a ${LOAD_LOG}
+date | tee -a ${LOAD_LOG}
diff --git a/snpmarker_weekly.sh b/snpmarker_weekly.sh
new file mode 100755
index 0000000..8d66392
--- /dev/null
+++ b/snpmarker_weekly.sh
@@ -0,0 +1,199 @@
+#!/bin/sh -x
+
+#
+# Program: snpmarker_weekly.sh
+#
+# Purpose:
+#       1) run snpmarker.sh to create new snp/marker associations in 
+#          a backend snp database
+#       2) create a backup of the source snp db
+#       3) load the backup into the destination snp db
+#
+# Usage:  snpmarker_weekly.sh [-a] [-r] [-c] [-l]
+#         where:
+#             -a is an option to archive output directory
+#             -r is an option to archive logs directory
+#             -c is an option to clean output directory
+#             -l is an option to clean logs directory
+#
+# History
+#
+# lec 06/30/2006 - modified for mgiconfig
+# 
+# sc    05/01/2006 - updated to bourne shell
+#		   - added optional archiving and directory cleaning
+#                    for logs and output dirs
+#		   - updated to use new bcpin_withTruncateDropIndex.csh
+# sc    03/27/2006 - created
+
+#
+#  Set up a log file for the shell script in case there is an error
+#  during configuration and initialization.
+#
+cd `dirname $0` 
+LOG=`pwd`/`basename $0`.log
+rm -f ${LOG}
+ 
+echo date | tee -a ${LOG}
+#
+#  Verify the argument(s) to the shell script.
+#
+ARC_OUTPUT=no
+ARC_LOGS=no
+CLEAN_OUTPUT=no
+CLEAN_LOGS=no
+
+usage="Usage: snpmarker_weekly.sh [-a] [-r] [-c] [-l]"
+
+#
+# report usage if there are unrecognized arguments
+#
+set -- `getopt arcl $*`
+if [ $? != 0 ]
+then
+    echo ${usage} | tee -a ${LOG}
+    exit 1
+fi
+
+#
+# determine which options on command line
+#
+for i in $*
+do
+    case $i in
+        -a) ARC_OUTPUT=yes; shift;;
+        -r) ARC_LOGS=yes; shift;;
+        -c) CLEAN_OUTPUT=yes; shift;;
+        -l) CLEAN_LOGS=yes; shift;;
+        --) shift; break;;
+    esac
+done
+
+#
+#  Establish the configuration file name, if readable source it
+#
+CONFIG_LOAD=`pwd`/Configuration
+if [ ! -r ${CONFIG_LOAD} ]
+then
+    echo "Cannot read configuration file: ${CONFIG_LOAD}" | tee -a ${LOG}
+    exit 1
+fi
+
+. ${CONFIG_LOAD}
+
+#
+#  Source the DLA library functions.
+#
+if [ "${DLAJOBSTREAMFUNC}" != "" ]
+then
+    if [ -r ${DLAJOBSTREAMFUNC} ]
+    then
+        . ${DLAJOBSTREAMFUNC}
+    else
+        echo "Cannot source DLA functions script: ${DLAJOBSTREAMFUNC}" | tee -a ${LOG}
+        exit 1
+    fi
+else
+    echo "Environment variable DLAJOBSTREAMFUNC has not been defined." | tee -a ${LOG}
+    exit 1
+fi
+
+#
+# archive/clean the logs and/or output directories?
+#
+if [ ${ARC_OUTPUT} = "yes" ]
+then
+    date | tee -a ${LOG}
+    echo "archiving  output directory" | tee -a ${LOG}
+    createArchive ${ARCHIVEDIR}/output ${CACHEDATADIR}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "createArchive for output directory failed" | tee -a ${LOG}
+        exit 1
+    fi
+fi
+
+if [ ${CLEAN_OUTPUT} = "yes" ]
+then
+    date | tee -a ${LOG}
+    echo "cleaning  output directory" | tee -a ${LOG}
+    cleanDir ${CACHEDATADIR}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "cleanDir for output directory failed" | tee -a ${LOG}
+        exit 1
+    fi
+
+fi
+
+if [ ${ARC_LOGS} = "yes" ]
+then
+    date | tee -a ${LOG}
+    echo "archiving logs directory" | tee -a ${LOG}
+    createArchive ${ARCHIVEDIR}/logs ${CACHELOGSDIR}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "createArchive for logs directory failed" | tee -a ${LOG}
+        exit 1
+    fi
+fi
+
+if [ ${CLEAN_LOGS} = "yes" ]
+then
+    date | tee -a ${LOG}
+    echo "cleaning logs directory" | tee -a ${LOG}
+    cleanDir ${CACHELOGSDIR}
+    STAT=$?
+    if [ ${STAT} -ne 0 ]
+    then
+        echo "cleanDir for logs directory failed" | tee -a ${LOG}
+        exit 1
+    fi
+fi
+
+date | tee -a ${LOG}
+
+#
+#   Establish the load log now that we have archived/cleaned
+#
+LOAD_LOG=${CACHELOGSDIR}/`basename $0`.log
+date | tee -a ${LOAD_LOG}
+
+cd ${CACHEDATADIR}
+
+#
+# run snpmarker.sh with no archive/clean to load the source db 
+#
+
+date | tee -a ${LOAD_LOG}
+echo "Calling ${CACHEINSTALLDIR}/snpmarker.sh" | tee -a ${LOAD_LOG}
+${CACHEINSTALLDIR}/snpmarker.sh
+STAT=$?
+if [ ${STAT} -ne 0 ]
+then
+     echo "${CACHEINSTALLDIR}/snpmarker.sh failed" | tee -a ${LOAD_LOG}
+     exit 1
+fi
+
+#
+# backup back end production snp database
+#
+echo "" | tee -a ${LOAD_LOG}
+date | tee -a ${LOAD_LOG}
+echo "Backing up ${SNPBE_DBSERVER}..${SNPBE_DBNAME}"
+${MGI_DBUTILS}/bin/dump_db.csh ${SNPBE_DBSERVER} ${SNPBE_DBNAME} ${SNP_BACKUP_LOCALPATH} | tee -a ${LOAD_LOG}
+
+#
+# load front-end snp database
+#
+echo "" | tee -a ${LOG}
+date | tee -a ${LOG}
+echo "Loading ${SNP_DBSERVER}..${SNP_DBNAME}"
+${MGI_DBUTILS}/bin/load_db.csh ${SNP_DBSERVER} ${SNP_DBNAME} ${SNP_BACKUP_REMOTEPATH} | tee -a ${LOAD_LOG}
+
+echo "" | tee -a ${LOAD_LOG}
+date | tee -a ${LOAD_LOG}
+
diff --git a/snpmrklocation.py b/snpmrklocation.py
deleted file mode 100755
index 1a4e1be..0000000
--- a/snpmrklocation.py
+++ /dev/null
@@ -1,94 +0,0 @@
-#!/usr/local/bin/python
-
-'''
-#
-# Purpose:
-#
-# Create bcp files for snp..MRK_Location_Cache
-#
-# Usage:
-#	snpmrklocation.py
-#
-# History
-#
-# 03/14/2006	sc created
-#
-'''
-
-import sys
-import os
-import db
-import mgi_utils
-import string
-import accessionlib
-
-NL = '\n'
-DL = '|'
-TAB = '\t'
-outputdir = os.environ['CACHEDATADIR']
-cacheTable = os.environ['MRKLOC_CACHETABLE']
-
-bcpFile = open('%s/%s.bcp' % (outputdir, cacheTable), 'w')
-
-def setup():
-        # set up connection to the mgd database
-        server = os.environ['MGD_DBSERVER']
-        mgdDB = os.environ['MGD_DBNAME']
-        user = os.environ['MGD_DBUSER']
-        password = string.strip(open(os.environ['MGD_DBPASSWORDFILE'], 'r').readline())
-        db.set_sqlLogin(user, password, server, mgdDB)
-
-def createBCP():
-	print 'Creating %s/%s.bcp' % (outputdir, cacheTable)
-	cmds = []
-        cmds.append('select * ' + \
-                'from MRK_Location_Cache')
-        results = db.sql(cmds, 'auto')
-	for r in results[0]:
-	    markerKey = r['_Marker_key']
-	    chromosome = r['chromosome']
-	    sequenceNum = r['sequenceNum']
-	    cytoOffset =  r['cytogeneticOffset']
-	    if cytoOffset == None:
-		cytoOffset = ''
-	    offset = r['offset']
-	    startCoord = r['startCoordinate']
-	    if startCoord == None:
-		startCoord = ''
-	    endCoord = r['endCoordinate']
-	    if endCoord == None:
-		endCoord = ''
-	    strand = r['strand']
-	    if strand == None:
-		strand = ''
-	    mapUnits = r['mapUnits']
-	    if mapUnits == None:
-		mapUnits = ''
-	    provider = r['provider']
-	    if provider == None:
-		provider = ''
-	    version = r['version']
-	    if version == None:
-		version = ''
-	    bcpFile.write(str(markerKey) + DL + \
-		str(chromosome) + DL + \
-	 	str(sequenceNum) + DL + \
-                str(cytoOffset) + DL + \
-                str(offset) + DL + \
-                str(startCoord) + DL + \
-                str(endCoord) + DL + \
-                str(strand) + DL + \
-                str(mapUnits) + DL + \
-                str(provider) + DL + \
-                str(version) + NL)
-	bcpFile.close()
-
-#
-# Main Routine
-#
-
-print '%s' % mgi_utils.date()
-setup()
-createBCP()
-print '%s' % mgi_utils.date()
-
diff --git a/snpmrkwithin.py b/snpmrkwithin.py
index ed56d93..30e9909 100755
--- a/snpmrkwithin.py
+++ b/snpmrkwithin.py
@@ -90,8 +90,11 @@
 # max number of lines per bcp file to avoid file > 2Gb
 MAX_BCP_LINES = string.atoi(os.environ['MAX_BCP_LINES'])
 
+# QTL Markery Type Key
+MRKR_QTLTYPE_KEY = string.atoi(os.environ['MRKR_QTLTYPE_KEY'])
+
 #
-# globals
+# GLOBALS
 #
 
 # number suffix for the current bcp file name
@@ -196,53 +199,15 @@ def initialize():
                      'from SNP_ConsensusSnp_Marker', 'auto')
 
     primaryKey = results[0]['key']
-    print 'primaryKey: %s' % primaryKey
-    openBCPFile()
-
-    return
-
-# Purpose: Creates a new bcp file pointer. Uses a counter to
-#          create a unique name
-# Returns: Nothing
-# Assumes: Nothing
-# Effects: Exits if can't open the new bcp file
-# Throws: Nothing
-
-def openBCPFile():
-    global fpSnpMrk
-    global snpMrkFileCtr
-    #global snpMrkFile
-
-    # append this to next bcp filename
-    snpMrkFileCtr = snpMrkFileCtr + 1
-    try:
-        fpSnpMrk = open("%s%s" % (snpMrkFile, snpMrkFileCtr),'w')
-    except:
-        sys.stderr.write('Could not open bcp file: %s\n' % snpMrkFile)
+    print 'primaryKey: %s' % primaryKey 
+    if primaryKey == None:
+	sys.stderr.write('SNP_ConsensusSnp_Marker table is ' + \
+              'empty, load dbSNP Marker associations first')
         sys.exit(1)
+    openBCPFile()
 
     return
 
-# Purpose: Perform cleanup steps for the script.
-# Returns: Nothing
-# Assumes: Nothing
-# Effects: Nothing
-# Throws: Nothing
-
-def finalize():
-    global fpSnpMrk
-
-    db.useOneConnection(0)
-
-    #
-    #  Close the bcp file.
-    #
-    fpSnpMrk.close()
-
-    return
-
-
-
 # Purpose: Create a bcp file with annotations for SNP/marker pairs where
 #          the SNP is within 1000 kb of the marker and there is no existing
 #          annotation for the SNP/marker.
@@ -275,6 +240,45 @@ def process():
 
     return
 
+# Purpose: Perform cleanup steps for the script.
+# Returns: Nothing
+# Assumes: Nothing
+# Effects: Nothing
+# Throws: Nothing
+
+def finalize():
+    global fpSnpMrk
+
+    db.useOneConnection(0)
+
+    #
+    #  Close the bcp file.
+    #
+    fpSnpMrk.close()
+
+    return
+
+# Purpose: Creates a new bcp file pointer. Uses a counter to
+#          create a unique name
+# Returns: Nothing
+# Assumes: Nothing
+# Effects: Exits if can't open the new bcp file
+# Throws: Nothing
+
+def openBCPFile():
+    global fpSnpMrk
+    global snpMrkFileCtr
+
+    # append this to next bcp filename
+    snpMrkFileCtr = snpMrkFileCtr + 1
+    try:
+        fpSnpMrk = open("%s%s" % (snpMrkFile, snpMrkFileCtr),'w')
+    except:
+        sys.stderr.write('Could not open bcp file: %s\n' % snpMrkFile)
+        sys.exit(1)
+
+    return
+
 # Purpose: Process all SNPs within the startCoord-endCoord range on the given
 #	   chr - by using binary search to find sub-regions with a small
 #	   enough number of SNPs (< MAX_NUMBER_SNPS) to process at a time
@@ -430,7 +434,8 @@ def processSNPregion(chr, startCoord, endCoord):
 		       'mc.endCoordinate "markerEnd", ' + \
 		       'mc.strand "markerStrand" ' + \
 		'from MRK_Location_Cache mc ' + \
-		'where mc.chromosome = "%s" and ' + \
+		'where mc._Marker_Type_key != %s and ' % MRKR_QTLTYPE_KEY + \
+		      'mc.chromosome = "%s" and ' + \
 		      'mc.endCoordinate >= %s and ' + \
 		      'mc.startCoordinate <= %s '
 
@@ -528,7 +533,7 @@ def processSNPmarkerPair(snp,	  # dictionary w/ keys as above
     # next available _SNP_ConsensusSnp_Marker_key
     global primaryKey
 
-    KB_DISTANCE = [ 2, 10, 100, 500, 1000 ]
+    #KB_DISTANCE = [ 2, 10, 100, 500, 1000 ]
 
     markerStart  = marker['markerStart']
     markerEnd    = marker['markerEnd']
@@ -539,6 +544,7 @@ def processSNPmarkerPair(snp,	  # dictionary w/ keys as above
     snpKey = snp['_ConsensusSnp_key']
     featureKey = snp['_Coord_Cache_key']
 
+    fxnKey = -1
     #
     #  The SNP is located within the coordinates of the marker.
     #
@@ -551,25 +557,25 @@ def processSNPmarkerPair(snp,	  # dictionary w/ keys as above
     #  distances from the marker. Check each distance (starting
     #  with the small range) to see which one it is.
     #
-    else:
-	sys.stdout.flush()
-	for kbDist in KB_DISTANCE:
-
-	    fxnKey = getKBTerm(snpLoc, markerStart, markerEnd,
-			       markerStrand, kbDist) 
-
-	    #
-	    #  If the distance has been determined, don't check
-	    #  any others.
-	    #
-	    if fxnKey > 0:
-		break
+    #else:
+    #	sys.stdout.flush()
+    #	for kbDist in KB_DISTANCE:
+    #
+    #	fxnKey = getKBTerm(snpLoc, markerStart, markerEnd,
+    #	       markerStrand, kbDist) 
+    #
+    #	    #
+    #           #  If the distance has been determined, don't check
+    #	        #  any others.
+    #       #
+    #    if fxnKey > 0:
+    #		break
     # if fxnKey can't be determined print msg to stdout
     # so it will be logged and return
     if fxnKey == -1:
-        print SNP_NOT_WITHIN % (snp, MARKER_PAD, marker)
-	sys.stdout.flush()
-	return
+        #print SNP_NOT_WITHIN % (snp, MARKER_PAD, marker)
+        #sys.sys.stdout.flush()
+        return
 
     # check the number of bcp lines in the current file, creating
     # new file if >= the configured max
@@ -645,7 +651,6 @@ def getKBTerm(snpLoc, markerStart, markerEnd, markerStrand, kbDist):
     #
     elif markerStrand == '-' and snpLoc > midPoint:
         direction = 'upstream'
-
     #
     #  If the SNP coordinate is <= the midpoint of the marker
     #  and strand is Null (MIT marker), the SNP is considered to be upstream.
diff --git a/system_docs/README b/system_docs/README
new file mode 100644
index 0000000..6a84483
--- /dev/null
+++ b/system_docs/README
@@ -0,0 +1 @@
+See dbsnpload/system_docs for documentation