Update bigsdb.conf file.

conf/bigsdb.conf

@@ -2,37 +2,120 @@
 #Set the attributes in this file specific to your system
 
 ###GENERAL####
-#tmp_dir:        Location of web accessible temporary directory
-#secure_tmp_dir: Location of web-inaccessible temporary directory
-#prefs_db:       Name of preference database
-#auth_db:        Name of authentication database
 
-tmp_dir=/home/httpd/pubmlst.org/tmp
+#Location of web accessible temporary directory.
+tmp_dir=/var/www/tmp
+
+#Location of web-inaccessible temporary directory.
 secure_tmp_dir=/var/tmp
+
+#Location of web accessible submission directory.
+submission_dir=/var/submissions
+
+#SMTP server for sending submission E-mail updates.
+#Comment out to disable.
+smtp_server=127.0.0.1
+
+#Name of preference database.
 prefs_db=bigsdb_prefs
+
+#Name of authentication database.
 auth_db=bigsdb_auth
 
+#Relative web paths to scripts - needed by submission system to move between
+#the two.  These do not need to be set if submission handling is not enabled.
+curate_script=/cgi-bin/private/bigsdb/bigscurate.pl
+query_script=/cgi-bin/bigsdb/bigsdb.pl
+
+#Specify number of days that job files will remain on server.
+results_deleted_days=7
+
+#Specify number of days before sequence BLAST database cache is marked stale.
+cache_days=7
+
+#Set intranet to 'yes' if clients are running without an internet connection
+#(jQuery and jQuery UI libraries are otherwise downloaded from Google CDN).
+#Ensure that the jquery.js and jquery-ui.js libraries are placed in /javascript
+#directory. These can be downloaded from:
+#http://ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js
+#[rename to jquery.js]
+#http://ajax.googleapis.com/ajax/libs/jqueryui/1.10.2/jquery-ui.min.js
+#[rename to jquery-ui.js]
+intranet=no
+
+#Set disable_updated to 'yes' to lock the curation interface during server
+#maintenance.
+disable_updates=no
+
+#Message to display during server maintenance.
+disable_update_message=
+
+#URL root to web-accessible documentation.
+doclink=http://bigsdb.readthedocs.org/en/latest
+
+###REST INTERFACE###########
+
+#Name of database describing resources for REST interface
+rest_db=bigsdb_rest
+
+#Is the REST interface using a PROXY server?
+rest_behind_proxy=0
+
+###OFFLINE JOB PROCESSING###
+
+#Name of offline job queue database (if you set this you'll also need to run
+#bigsjobs.pl from a CRON job frequently). If not set, plugins that rely on
+#offline processing will be unavailable.
+jobs_db=bigsdb_jobs
+
+#Do not start job if load average (over last minute) is greater than value.
+max_load=8
+
 ####EMBOSS####
-#Path of directory containing EMBOSS programs - used for sequence alignment in allele query
+#used for sequence alignment in allele query
+
+emboss_path=/usr/bin
+
+####BLAST+ BIN DIRECTORY
+#Path of directory containing BLAST+ binaries (blastn, blastx, tblastx,
+#makeblastdb). It is recommended that you use statically-linked binaries
+#downloaded from NCBI.
 
-emboss_path=/usr/software/EMBOSS/EMBOSS/emboss/bin
+blast+_path=/usr/local/ncbi-blast+/bin
 
-####BLAST BIN DIRECTORY
-#Path of directory containing BLAST (blastall and formatdb) programs
-
-blast_path=/usr/local/bin
+####MAXIMUM NUMBER OF BLAST THREADS
+#Do not set to > number of processor cores
+blast_threads=1
 
 ####MUSCLE#####
 #Path of muscle executable
 
 muscle_path=/usr/bin/muscle
 
+####MAFFT######
+#Path of mafft executable
+#Must be version 6.840 or higher
+
+mafft_path=/usr/bin/mafft
+mafft_threads=1
+
+####IPCRESS####
+#Path of ipcress executable
+
+ipcress_path=/usr/bin/ipcress 
+
+####MOGRIFY####
+mogrify_path=/usr/bin/mogrify
+
+####SPLITSTREE#
+splitstree_path=/usr/bin/splitstree4
+
 ##REFERENCE DB#
 #Set to reference dbase name 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)
 
-refdb=refs
+ref_db=bigsdb_refs
 
 #CHARTDIRECTOR####
 #Set to 1 if the chartdirector library is installed