#BIGSdb site-specific configuration file #Set the attributes in this file specific to your system ###GENERAL#### #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#### #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. blast+_path=/usr/local/ncbi-blast+/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) ref_db=bigsdb_refs #CHARTDIRECTOR#### #Set to 1 if the chartdirector library is installed chartdirector=1