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).

For maintainers of the 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 2.14.1+.

PRIMER3

https://github.com/primer3-org/primer3/releases

The current version of j5 works well with the Primer3 v2.6.1 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

Note for UUID - at least on Mac OSX (e.g. 15.5) - UUID would not install sucessfully as the default configuration was not finding "EXTERN.h". I had to add this line to my .bashrc - "export CPATH=/Library/Developer/CommandLineTools/SDKs/MacOSX15.5.sdk/System/Library/Perl/5.34/darwin-thread-multi-2level/CORE/" to point the compiler to where EXTERN.h was.

IPC::Run

Hash::Merge

Try::Tiny

XML::TreePP