#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 secure temporary directory. #Beware if your system uses systemd PrivateTmp - this may cause problems if you #use /var/tmp since apache won't see files created by scripts run as the bigsdb #user. This will affect the use of manually refreshed BLAST database caches. #In this case it is better to use a temporary directory outside of /tmp #or /var/tmp. Alternatively, disable the use of PrivateTmp by apache. secure_tmp_dir=/var/tmp #Location of web accessible submission directory. submission_dir=/var/submissions #Directory used to contain system lock files lock_dir=/var/run/lock #Site administrator E-mail address (optional) #This is used for site-wide account administration if there are problems. #site_admin_email=admin@your_domain.com #Site user databases #Set name of global user database - this is optional. If this is not used #then each database will maintain its own set of user details. Usually #only one database will be specified here, but multiple databases are #supported (enter a comma-separated list of user databases - each consisting #of a display name, followed by a pipe character (|) and the name of the #database). #site_user_dbs=PubMLST|pubmlst_bigsdb_users #Site-wide accounts #Allow users to request registration (set to 1 to enable). auto_registration=0 new_account_validation_timeout_mins=60 inactive_account_removal_days=180 ;registration_address=https://pubmlst.org/bigsdb #SMTP server for sending E-mail updates (submissions and offline jobs). #smtp_server=127.0.0.1 #smtp_port=25 domain=pubmlst.org #Name of preference database. prefs_db=bigsdb_prefs #Name of authentication database. auth_db=bigsdb_auth #Web-accessible path to stylesheet. Needed only for viewing offline content #generated by plugins such as LocusExplorer. Default setting will be used #unless uncommented. #stylesheet=https://pubmlst.org/css/bigsdb.css #Relative web paths to scripts - needed by submission system and private to #move between the two and if private record uploads is 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 #Disable the 'this site uses cookies' message. no_cookie_consent=0 #Set disable_updated to '1' to lock the curation interface during server #maintenance. disable_updates=0 #Message to display during server maintenance. #disable_update_message=This server is undergoing maintenance. #URL root to web-accessible documentation. doclink=http://bigsdb.readthedocs.io/en/latest #Maximum file upload size (MB) max_upload_size=32 #Set PostgreSQL temporary buffers (MB) - likely to be needed if using cgMLST #schemes. Alternatively this can be set globally in postgresql.conf. temp_buffers=64 #Force retirement of id when deleting isolate, profile or allele records delete_retire_only=0 ###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 #Hide E-mail addresses of curators in REST interface (sender E-mails are #hidden by default) rest_hide_emails=0 #Set to log all REST calls to the rest_db. You should set a CRON job to remove #calls older than a specified time, e.g. 7 days, to prevent this log getting #too big. rest_log_to_db=0 #The following are just used to colour the dashboard numbers on the REST monitor. #Numbers will incrementally change from blue to red as they increase. Numbers #greater than those set below will be the same colour as the max value. max_rest_hits_per_second_warn=10 max_avg_response_warn=500 ###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 #Do not start web-based tag scanning if load average (over last minute) is greater than value. Set lower than max_load to prevent web scans blocking #normal sequence queries (max_load value is used if not set). #max_load_webscan=6 #Record status of scripts such as the autotagger, autodefiner and cache renewal #in the jobs database. Set if you want these to be included in the jobs #monitor. record_scripts=0 #Record status of manual web scans in the jobs database. Set if you want these #to be included in the jobs monitor. record_scans=0 #The following are just used to colour the dashboard numbers on the job monitor. #Numbers will incrementally change from blue to red as they increase. Numbers #greater than those set below will be the same colour as the max value. max_queued_colour_warn=10 max_running_colour_warn=10 ####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 and maximum memory it can use (MB) muscle_path=/usr/bin/muscle max_muscle_mb=4096 ####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 ####CLUSTALW### clustalw_path=/usr/bin/clustalw ####BLAT####### #Only needed if working with eukaryote genomes containing introns #blat_path=/usr/local/bin/blat ##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 #EXPORT########### #Threshold for number of records before export job is sent to the offline job #manager instead of running immediately. ;export_instant_run=2000 #GENOME COMPARATOR #It is recommended that you use at least 2 threads. It is not currently #possible to cancel a running job when only a single thread is used. genome_comparator_limit=1000 genome_comparator_threads=2 #ITOL############# itol_record_limit=2000 itol_seq_limit=100000 #MICROREACT####### microreact_record_limit=2000 microreact_seq_limit=100000 #PHYLOVIZ######### #Enter Phyloviz account details - these need to be registered with PhyloViz ;phyloviz_user=xxxxxxxx ;phyloviz_passwd=xxxxxxxx #GrapeTree######## #Install GrapeTree from https://github.com/achtman-lab/GrapeTree #Set location for installation directory 'grapetree_path'. #Copy MSTree_holder.html to a directory in the website and list its location #relative to the root of the website 'MSTree_holder_rel_path'. #The 'static' directory should be a sub-directory of the directory containing #MSTree_holder.html ;python3_path=/usr/bin/python3 ;grapetree_path=/usr/local/GrapeTree ;MSTree_holder_rel_path=/GrapeTree/MSTree_holder.html grapetree_limit=10000 #GENEPRESENCE####### genepresence_taxa_limit=10000 genepresence_record_limit=500000