Packages required for j5

Very few j5 users (-if any- need to) install j5 on their own computer, since the functionality is accessible via DIVA (e.g. https://public-diva.jbei.org) and a basic web interface for j5 is also accessible (https://j5.jbei.org/). In addition, the j5 XML-RPC web-service gives users access to the full functionality of j5 through XML-RPC thin client software.


For maintainers of the public j5 server and/or DIVA servers, though, here are the software packages that are required for an installation of j5:


BLAST (bl2seq):

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

The current version of j5 works well with standalone BLAST 2.9.0+.


PRIMER3

https://sourceforge.net/projects/primer3/files/primer3/

The current version of j5 works well with the Primer3 v2.4.0 release.


The following perl modules may be easily installed through the command line: perl -MCPAN -e 'install module_name'

The CPAN shell can also be initiated through the command line: perl -MCPAN -e shell


BioPerl

Available via CPAN (e.g.):

CJFIELDS/BioPerl-1.7.8.tar.gz

CJFIELDS/BioPerl-Run-1.007003.tar.gz

within the CPAN shell, you can run the command: i /bioperl/ to find the most recent versions...

The current version of j5 works well with the BioPerl-1.7.8 release and BioPerl-Run-1.007003 release.

Bio::Perl

Bio::Tools::Run::Primer3Redux


Additional perl modules:

Text::CSV_PP

Archive::Zip

Archive::Extract

UUID

IPC::Run

Hash::Merge

Try::Tiny

XML::TreePP


For the j5 XML-RPC web server, you'll also need the following:

XML::RPC

MIME::Base64

LWP::UserAgent


For client-side access the j5 XML-RPC service running under SSL (via https://) it is also necessary that you have the perl modules installed on the client machine:

IO::Socket::SSL

Crypt::SSLeay