The Dintegrator project/tools depend on the following external packages. See Notes on Mac OS X installation for some details on Mac OS X installation. For some packages, Mac OS X is mentioned again.
Python (>= 3.7)
Perl (>= 5.10)
- Class::InsideOut (libclass-insideout-perl)
- Config::IniFiles (libconfig-inifiles-perl)
- Error (liberror-perl)
- Getopt::Long::Descriptive (libgetopt-long-descriptive-perl)
- Log::Log4perl (liblog-log4perl-perl)
- Readonly (libreadonly-xs-perl)
- List::MoreUtils (liblist-moreutils-perl)
- Text::CSV_XS (libtext-csv-xs-perl)
Doxygen (>= 1.6)
- doxypy
- Doxygen::Filter::Perl (doxygen-filter-perl):
- Pod::POM (libpod-pom-perl)
- Log::Log4perl (liblog-log4perl-perl)
Ensembl API interface
Current version of Ensembl API (http://www.ensembl.org/info/docs/api/api_installation.html and ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz), which depends on:
- Bio::Perl (bioperl => 1.6.901)
- DBI (libdbi-perl)
- DBD::mysql (libdbd-mysql-perl)
- Set::IntervalTree (libset-intervaltree-perl)
- Sereal (libsereal-perl)
- Role::Tiny::With
- JSON
- JSON::XS
- IO::Socket::SSL (see IO::Socket::SSL in Notes on Mac OS X installation)
- CGI
- LWP::Simple
- Bio::DB::HTS (see notes on Bio::DB::HTS)
- Tabix.pm and the binary 'tabix' in $PATH (See notes on Tabix.) This is different from Bio::DB::HTS::Tabix!
If Galaxy is being deployed, all the past EnsEMBL releases are required to be installed too, according to the layout described in EnsEMBL API installation. The required releases are
- EnsEMBL 67
- EnsEMBL 68
- EnsEMBL 69
- EnsEMBL 70
- EnsEMBL 71
- EnsEMBL 72
- EnsEMBL 73
- EnsEMBL 74
- EnsEMBL 75
- EnsEMBL 84
- EnsEMBL 88
- EnsEMBL 95
If you are installing from a downloaded package, the Ensembl API is already set up as needed, just follow the instructions in the README file contained in the downloaded tarball.
Extra dependencies
For XML validation in the Galaxy test-suite you need either:
