j5 installation

Users will not need to install j5 on their own computer, since the public web interface for the software is accessible at: https://public-diva.jbei.org.

Installation of the core j5 package:

These steps may require contacting your information technology support staff for assistance. The basic steps are to: 1) make sure that the software packages required for j5 are already properly installed (and accessible in your executable path, if applicable, see below), 2) download the j5 perl modules (you'll need to contact the j5 team in order to do this), 3) edit the j5 configuration perl modules to reflect the your local installation, and 4) place the j5 perl modules in to your local BioPerl package library directory structure (e.g. /Library/Perl/5.30/Bio/Tools/).

Installing required additional perl modules from CPAN (e.g. Text::CSV_PP)

Note that installing these required modules from CPAN is greatly facilitated with the following command:

sudo perl -MCPAN -e 'install Text::CSV_PP'

which will install the Text::CSV_PP perl module(s) automatically. The "Text::CSV_PP" can be substituted with any other perl module that you would like/need to install.

Executables that must be accessible in the search PATH:

The BLAST bl2seq executable (e.g. blastn)

The Primer3 executable (e.g. primer3_core)

The j5 perl modules should be placed in the same directory as the BioPerl package, (e.g. /Library/Perl/5.30/Bio/Tools/).

Contained within this Bio/Tools/ BioPerl directory should be the following (in addition to the other BioPerl modules):

j5.pm - the core j5 perl module

j5/Automation.pm - a j5 perl module that manages downstream automation processes

j5/Auxiliary.pm - a j5 perl module that manages auxiliary processes

j5/Configuration.pm - a j5 perl module that configures the j5 package

The j5/Configuration.pm perl module must be modified as following:

The lines containing

PATHTOBLASTANDPRIMER3 => ":/usr/local/ncbi/blast/bin:/usr/local/share/primer3/bin",

PATHTOPRIMER3EXECUTABLE => "/usr/local/share/primer3/bin/primer3_core",

PATHTOPRIMER3CONFIG => "/usr/local/share/primer3/bin/primer3_config",

J5_WWW_DIRECTORY => '/var/www/j5',

MAXTHREADS => 8

should be modified to reflect the paths to the BLAST and Primer3 directories, to the primer3 executable, to the primer3 configuration directory, to the j5 server www directory (see below), and how many threads to use (e.g. to process assembly piece compatibility checks in parallel).

The following perl scripts that call the j5 software package must be accessible in your executable PATH:

j5_SLIC_Gibson_CPEC.pl

j5_SLIC_Gibson_CPEC_zip.pl

j5_combinatorial_SLIC_Gibson_CPEC.pl

j5_combinatorial_SLIC_Gibson_CPEC_zip.pl

j5_golden_gate.pl

j5_golden_gate_zip.pl

j5_combinatorial_golden_gate.pl

j5_combinatorial_golden_gate_zip.pl

j5_mock_zip.pl

j5_combinatorial_mock_zip.pl

j5_condense_assembly_files.pl

j5_condense_assembly_files_zip.pl

j5_distribute_pcr_reactions.pl

j5_distribute_pcr_reactions_zip.pl

j5_distribute_split_and_pool_pcr_reactions.pl

j5_distribute_split_and_pool_pcr_reactions_zip.pl

jbeiseq_to_genbank.pl

genbank_to_jbeiseq.pl

SBOLXML_to_genbank.pl

genbank_to_SBOLXML.pl

The j5 web-server directory should be placed at the root of the path accessible by the web server, (e.g. /var/www/j5).

bin/ - a directory containing the j5 perl-cgi scripts.

The j5 web-server cgi-bin directory (e.g. /var/www/bin) should contain the following:

j5_check_for_assembly_piece_incompatibilities.pl - a perl script that is used to check for assembly piece incompatibilities in multi-threaded mode