dependencies.rst

BIGSdb dependencies

Required packages

BIGSdb requires a number of software components to be installed:

Linux packages

• Apache2 web server with mod_perl2
• PostgreSQL database 9.5+
• Perl 5.10+
• 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.

Perl modules

These are included with most Linux distributions.

• Archive::Zip - Used to upload to iTOL.
• Bio::Biblio - This used to be part of BioPerl but will need to be installed separately if using BioPerl 1.6.920 or later.
• CGI (version 4.04+) - Common Gateway Interface requests and responses (used to be a core module but recently removed).
• Config::Tiny - Configuration file handling.
• Crypt::Eksblowfish::Bcrypt - Used for password hashing.
• Data::Random
• Data::UUID - Globally unique identifer handling for preference storage.
• DBD::Pg - PostgreSQL database driver for DBI.
• DBI - Database independent interface - module used to interact with databases.
• Email::MIME - Used to format E-mail messages.
• Email::Sender - Used to send E-mail messages by submission system.
• Email::Valid - Used to validate E-mails sent by job manager.
• Excel::Writer::XLSX - Used to export data in Excel format.
• Exception::Class - Exception handing.
• File::Map
• File::Type - Used to determine what type of file has been uploaded.
• IO::String
• JSON - Used to manipulate JSON data.
• List::MoreUtils (version 0.28+).
• Log::Dispatch::File - Object for logging to file.
• Log::Log4perl - Configurable status and error logging.
• LWP::UserAgent - Used to upload via API
• Net::Oauth - Required for REST authentication (this needs to be installed even if you are not using REST).
• Parallel::ForkManager - Required for multi-threading tools and plugins.
• PDL - Required for LINcode calculations.
• Time::Duration - Used by Job Viewer to display elapsed time in rounded units.
• TOML - Used to define dashboard layouts.
• Try::Tiny
• XML::Parser::PerlSAX - part of libxml-perl - Used to parse XML configuration files.

Optional packages

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

• ImageMagick - mogrify used by some plugins.
• MAFFT 6.8+ - sequence alignment used by some plugins.
• Muscle - sequence alignment used by some plugins.
• Splitstree4 - used by GenomeComparator plugin.