BIGSdb requires a number of software components to be installed:
- Apache2 web server with mod_perl2
- PostgreSQL database
- 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
- Data::UUID - Globally unique identifer handling for preference storage
- 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.
- ChartDirector - library used for generating charts. Used by some plugins.
- ImageMagick - mogrify used by some plugins.
- MAFFT - sequence alignment used by some plugins.
- Muscle - sequence alignment used by some plugins.
- Splitstree4 - used by GenomeComparator plugin.