23 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