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Packages required for j5
As noted in the following j5 installation documentation page, users will not need to install j5 on their own computer, since a web interface for the software is accessible at:
https://j5.jbei.org/

In addition, the j5 XML-RPC web-service allows users to utilize the full functionality of j5 through locally installed XML-RPC thin client software, without having to install and maintain j5 on their own machines.

There are several software packages that are required for a local installation of the j5 automated DNA assembly software package to function properly:

BLAST (bl2seq):
Available at:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

The current version of j5 works well with standalone BLAST 2.9.0+. Note that earlier versions of the standalone BLAST package (e.g. 2.2.21) have a different interface and will not be compatible with the current version of j5.

PRIMER3:
Available at:
https://sourceforge.net/projects/primer3/files/primer3/

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

BioPerl:
Available at:
https://metacpan.org/release/BioPerl
https://metacpan.org/release/BioPerl-Run

The current version of j5 works well with the BioPerl-1.7.5 release and BioPerl-Run-1.007003 release.

Bio::Tools::Run::Primer3Redux
Available at:
https://metacpan.org/pod/Bio::Tools::Run::Primer3Redux

The current version of j5 works well with the Bio-Tools-Primer3Redux-0.09 release.

Please contact Chris Fields ([email protected]) for more information.

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

Text::CSV_PP
A perl module available at:
https://metacpan.org/pod/distribution/Text-CSV_XS/CSV_XS.pm

Archive::Zip
A perl module available at:
https://metacpan.org/pod/release/ADAMK/Archive-Zip-1.31_04/lib/Archive/Zip.pm

Archive::Extract
A perl module available at:
https://metacpan.org/pod/distribution/Archive-Extract/lib/Archive/Extract.pm

UUID
A perl module available at:
https://metacpan.org/pod/release/JNH/UUID-0.04/UUID.pm

IPC::Run
A perl module available at:
https://metacpan.org/pod/distribution/IPC-Run/lib/IPC/Run.pm

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

XML::RPC
A perl module available at:
https://metacpan.org/pod/release/DAAN/XML-RPC-0.9/lib/XML/RPC.pm

MIME::Base64
A perl module available at:
https://metacpan.org/pod/release/GAAS/MIME-Base64-3.13/Base64.pm

LWP::UserAgent
A perl module available at:
https://metacpan.org/pod/release/GAAS/libwww-perl-6.05/lib/LWP/UserAgent.pm

Hash::Merge
A perl module available at:
https://metacpan.org/pod/release/DMUEY/Hash-Merge-0.12/Merge.pm

Try::Tiny
A perl module available at:
https://metacpan.org/pod/release/DOY/Try-Tiny-0.18/lib/Try/Tiny.pm

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
A perl module available at:
https://metacpan.org/pod/release/SULLR/IO-Socket-SSL-2.006/lib/IO/Socket/SSL.pod

Crypt::SSLeay
A perl module available at:
https://metacpan.org/pod/distribution/Crypt-SSLeay/SSLeay.pm