BIGSdb dependencies¶

Required packages¶

BIGSdb requires a number of software components to be installed:

Apache2 web server with mod_perl2
PostgreSQL database
Perl
BioPerl
BLAST+
EMBOSS
- infoalign - use to extract alignment stats in Genome Comparator.
- sixpack - used to translate sequences in multiple reading frames.
- stretcher - used for sequence alignment in allele query.
Ipcress - part of exonerate package - used to simulate PCR reactions which can be used to filter the genome to predicted amplification products.
Xvfb - X virtual framebuffer - needed to support SplitsTree in command line mode as used in Genome Comparator.

These are included with most Linux distributions.

DBI - Database Independent interface - module used to interact with databases.
DBD-Pg - PostgreSQL database driver for DBI.
XML::Parser::perlSAX - part of libxml-perl - Used to parse XML configuration files.
Log::Log4perl - Configurable status and error logging
Log::Dispatch::File - Object for logging to file
Error - Exception handling
Config::Tiny - Configuration file handling
Bio::Biblio - this used to be part of BioPerl but will need to be installed separately if using BioPerl 1.6.920 or later
IO::String
Data::UUID - Globally unique identifer handling for preference storage
List::MoreUtils
Time::Duration [optional] - Used by Job Viewer to display elapsed time in rounded units
Excel::Writer::XLSX - Used to export data in Excel format
Parallel::ForkManager - Required for multi-threading autotagger and autodefiner scripts.

Installing these packages will enable extra functionality, but they are not required by the core BIGSdb package.