60 Stand alone command line interface In addition to web services and graphical user interfaces, the j5 software package is also accessible via the command line. There are two different sets of perl scripts used to access the j5 software package from the command line. The first set (which includes j5_SLIC_Gibson_CPEC.pl, j5_combinatorial_SLIC_Gibson_CPEC.pl, j5_golden_gate.pl, j5_combinatorial_golden_gate.pl, j5_condense_assembly_files.pl, j5_distribute_pcr_reactions.pl) places the resulting new output files (and appends to/updates the master plasmids, oligos direct syntheses, source plate list, and zipped plate files input files) in the current working directory, and affects the master plasmids, oligos and direct syntheses list files in the current working directory. The second set (which includes j5_SLIC_Gibson_CPEC_zip.pl, j5_combinatorial_SLIC_Gibson_CPEC_zip.pl, j5_golden_gate_zip.pl, j5_combinatorial_golden_gate_zip.pl,  j5_condense_assembly_files_zip.pl, and j5_distribute_pcr_reactions_zip.pl) places the resulting output in a zip file (whose file name contains an embedded time stamp) in directory username/yearmonthday/hour/ (relative to the current working directory, where username is the login name of the current user), and does not affect the master plasmids, oligos and direct syntheses list files in the current working directory. j5_SLIC_Gibson_CPEC.pl, j5_combinatorial_SLIC_Gibson_CPEC.pl, j5_golden_gate.pl, and j5_combinatorial_golden_gate.pl: Usage: j5_program j5ParametersFileName SequencesListFileName PartsListFileName TargetPartOrderListFileName EugeneRulesListFileName MasterPlasmidsListFileName MasterOligosListFileName MasterDirectSynthesesListFileName The input files specified on the command line should be formatted as specified in the j5 input files documentation section, and should be located in the current working directory. Input files which should also be located in the current working directory (but are not explicitly specified on the command line) include the sequence files contained in the sequences list input file. The resulting output (placed in the current working directly) includes a new j5 assembly (.csv) file and a new genbank (.gb) or fasta (.fas) file for each designed plasmid (only one in the case of j5_SLIC_Gibson_CPEC.pl or j5_golden_gate.pl, and one or more in the case of j5_combinatorial_SLIC_Gibson_CPEC.pl or j5_combinatorial_golden_gate.pl), as well as new condensed combinatorial j5 assembly (.csv) file in the case of j5_combinatorial_SLIC_Gibson_CPEC.pl or j5_combinatorial_golden_gate.pl; the master plasmids, oligos and direct syntheses list files in the current working directory are also updated. Please see the j5 output files documentation section for more details. j5_condense_assembly_files.pl: Usage: j5_condense_assembly_files.pl AssemblyFilesToCondenseFileName The input file specified on the command line should be formatted as specified in the j5 input files documentation section, and should be located in the current working directory. Input files which should also be located in the current working directory (but are not explicitly specified on the command line) include the assembly files listed in the assembly files to condense input file. The resulting output (placed in the current working directly) includes a new j5 condensed assembly (.csv) file. Please see the j5 output files documentation section for more details. j5_distribute_pcr_reactions.pl: Usage: j5_distribute_pcr_reactions.pl DownstreamAutomationParametersFileName PlateListFileName AssemblyToAutomateFileName The input files specified on the command line should be formatted as specified in the j5 input files documentation section, and should be located in the current working directory. Input files which should also be located in the current working directory (but are not explicitly specified on the command line) include the plate files listed in the plate files list input file. The resulting output (placed in the current working directly) includes updated plate list and plate files files, and new distribute PCR reaction and NextGen control (.csv) files. Please see the j5 output files documentation section for more details. j5_distribute_split_and_pool_pcr_reactions.pl: Usage: j5_distribute_split_and_pool_pcr_reactions.pl DownstreamAutomationParametersFileName PlateListFileName AssemblyToAutomateFileName The input files specified on the command line should be formatted as specified in the j5 input files documentation section, and should be located in the current working directory. Input files which should also be located in the current working directory (but are not explicitly specified on the command line) include the plate files listed in the plate files list input file. The resulting output (placed in the current working directly) includes updated plate list and plate files files, and new distribute PCR reaction (.csv) and PR-PR (.pr) files. Please see the j5 output files documentation section for more details. j5_SLIC_Gibson_CPEC_zip.pl, j5_combinatorial_SLIC_Gibson_CPEC_zip.pl, j5_golden_gate_zip.pl, and j5_combinatorial_golden_gate_zip.pl: Usage: j5_program j5ParametersFileName SequencesListFileName ZippedSequencesFileName PartsListFileName TargetPartOrderListFileName EugeneRulesListFileName MasterPlasmidsListFileName MasterOligosListFileName MasterDirectSynthesesListFileName The input files specified on the command line should be formatted as specified in the j5 input files documentation section, and should be located in the current working directory. The resulting output (placed in the directory username/yearmonthday/hour/ (relative to the current working directory, where username is the login name of the current user)) includes a new zip file (whose file name contains an embedded time stamp) that contains the input files used in the assembly, a new j5 assembly (.csv) file and a new genbank (.gb) or fasta (.fas) file for each designed plasmid (only one in the case of j5_SLIC_Gibson_CPEC_zip.pl or j5_golden_gate_zip.pl, and one or more in the case of j5_combinatorial_SLIC_Gibson_CPEC_zip.pl or j5_combinatorial_golden_gate_zip.pl), a new condensed combinatorial j5 assembly (.csv) file in the case of j5_combinatorial_SLIC_Gibson_CPEC_zip.pl or j5_combinatorial_golden_gate_zip.pl, as well as updated master plasmids, oligos and direct syntheses list files. Please see the j5 output files documentation section for more details. j5_condense_assembly_files_zip.pl: Usage: j5_condense_assembly_files_zip.pl AssemblyFilesToCondenseFileName ZippedAssemblyFilesFileName The input files specified on the command line should be formatted as specified in the j5 input files documentation section, and should be located in the current working directory. The resulting output (placed in the directory username/yearmonthday/hour/ (relative to the current working directory, where username is the login name of the current user)) includes a new zip file (whose file name contains an embedded time stamp) that contains the input files used to generate the condensed assembly file and a new j5 condensed assembly (.csv) file. Please see the j5 output files documentation section for more details. j5_distribute_pcr_reactions_zip.pl: Usage: j5_distribute_pcr_reactions_zip.pl DownstreamAutomationParametersFileName PlateListFileName ZippedPlateFilesFileName AssemblyToAutomateFileName The input files specified on the command line should be formatted as specified in the j5 input files documentation section, and should be located in the current working directory. The resulting output (placed in the directory username/yearmonthday/hour/ (relative to the current working directory, where username is the login name of the current user)) includes a new zip file (whose file name contains an embedded time stamp) that contains updated plate list and zipped plate files input files, and new distribute PCR reaction and NextGen control (.csv) files. Please see the j5 output files documentation section for more details. j5_distribute_split_and_pool_pcr_reactions_zip.pl: Usage: j5_distribute_split_and_pool_pcr_reactions_zip.pl DownstreamAutomationParametersFileName PlateListFileName ZippedPlateFilesFileName AssemblyToAutomateFileName The input files specified on the command line should be formatted as specified in the j5 input files documentation section, and should be located in the current working directory. The resulting output (placed in the directory username/yearmonthday/hour/ (relative to the current working directory, where username is the login name of the current user)) includes a new zip file (whose file name contains an embedded time stamp) that contains updated plate list and zipped plate files input files, and new distribute PCR reaction (.csv) and PR-PR (.pr) files. Please see the j5 output files documentation section for more details.