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-1.7.7.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-1.7.7 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
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