###GENERAL####
profile_header=/usr/local/mlstdbnet/profile_header.html 
isolate_header=/usr/local/mlstdbnet/isolate_header.html
profile_footer=/usr/local/mlstdbnet/footer.html
isolate_footer=/usr/local/mlstdbnet/footer.html
tmp_dir=/var/www/html/tmp

####EMBOSS####
#used for sequence alignment in allele query
#set 'emboss=0' to remove functionality
emboss=1
emboss_path=/usr/local/bin

####JALVIEW####
#used for global sequence alignment in allele query
#and tree-drawing
jalview=1

####BIOPERL####
#Used for creating sequences in multiple formats.
#Set to 1 if BioPerl is installed
bioperl=1

####BLAST######
#Used for databases where sequences are of unequal
#length
blast=1
blast_path=/usr/local/blast/bin


##REFERENCE DB#
#Set to 1 if you have set up a local reference database.
#You will need to run the accompaning getrefs.pl script regularly to
#keep this updated (unless you're mirroring another system)
reference=1

###PRIVACY#####
#Set to 1 to hide the sender's E-mail address when displaying
#information on a strain.
privacy=1

###EXPORT######
#Set to 'export=1' to enable E-mail export of datasets.  Ensure that you have
#a valid SMTP server set (depending on your network, the server running
#this script may act as an SMTP server and the IP address 127.0.0.1 may
#work fine.  Set the export_sender address to include a valid domain
#or your mail server (or the recipient's) may reject it.  
#To log exports to a database, set 'exportlog=1' - make sure
#you have created a log database calleld 'export_log' using the provided
#SQL script.  
export=1
smtp_server=127.0.0.1
export_sender=mlstdb@medawar.ox.ac.uk
exportlog=1

#SEQ DOWNLOAD##
#Set to 1 to allow trace file download for profiles databases.
#This option also needs to be selected in the XML data description of
#the database - in the system attribute, set 'trace_dl="yes"'.
#Make a directory off the top level of your website called 'traces'.
#Place trace files in here - they should be named
#locus_allele_(F/R).scf e.g. aroE_5_R.scf.
trace_dl=1

#BCM TRACE VIEWER#
#Set to 1 to allow display of trace files for profiles databases if
#you've offered them for download.  You will need to install BCM
#trace viewer - install the java files to the java installation directory.
traceviewer=1

#CHARTDIRECTOR####
#Set to 1 if chartdirector software is installed
chartdirector=0

####DEBUG####
#Set to 0 to reduce messages in apache error log.  You should do
#this in production environments.  With this set to 0, the only log messages
#you should see are malicious SQL injection attempts.  Any other errors
#suggest a bug and should be reported.
debug=0