Note that install.pl attempts to install all of the packages below, and their dependencies, automatically.
###Perl Modules
####All users need these
- Benchmark
- Carp
- Capture::Tiny
- File::Basename
- File::Cat
- File::Copy
- File::Path
- File::Spec
- File::Util
- Getopt::Long
- IPC::System::Simple
- IO::Uncompress::Gunzip
- IO::Compress::Gzip
- List::Util
- Math::Random
- Parallel::ForkManager
- POSIX
- Unicode::UTF8
- XML::DOM
- XML::Tidy
###R Packages
- vegan
- ggplot2
- reshape2
- plyr
- fpc
- grid
- coin
- MASS
- qvalue (bioconductor)
- multtest (bioconductor)
- cluster
- psych
###Translation/Gene Annotation Tools
- Metatrans
- transeq
- prodigal
###Homology Detection Tools
- HMMER (v3)
- BLAST+
- LAST
- RAPsearch (v2)
###MySQL (Only if using a mysql database - advanced users only!)
- mysql 5.5 or greater
#####Perl Modules that are only needed if using a mysql database (advanced users)
- DBIx::Class
- DBIx::BulkLoader::Mysql
- DBI
- DBD::mysql
Note: if mysql server is on foreign machine, DBD::mysql may need to be installed by hand. see http://search.cpan.org/dist/DBD-mysql/lib/DBD/mysql/INSTALL.pod