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4.12 (Build 81) Apr 18, 2014

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Commandline Version and Commandline Options

COPASI comes in two versions. One (CopasiUI) with a GUI for interactive work and one (CopasiSE) without a GUI for batch processing of model files. Both versions support the same set of commandline arguments, although some do not make sense for the GUI version and will be ignored.

In addition to the commandline options, you can specify one or more COPASI (or Gepasi) files after the commandline options which will then be processed. Specifying more than one file again only makes sense for the commandline version of COPASI. For each of the files, the activated tasks will be run. The commandline options for importing and exporting SBML as well as the --save option are ignored if more than one file is specified. Since the GUI version of COPASI can only handle one file at a time, it only makes sense to specify one file after the commandline options.

Commandline Options
Option Argument Description
-s, --save string value This option is used to specify the name file where COPASI should store a model. This is useful if you intend to convert some SBML files to COPASI files in a batch job. This also makes sense only for the commandline version and will be ignored by the GUI version.
-i, --importSBML string value This options lets you specify an SBML file that COPASI shall import.
-e, --exportSBML string value With this option you can specify a name for the SBML file COPASI should export. This is useful if you want to export some COPASI files to SBML in a batch job. This only makes sense for the commandline version and it will be ignored by the GUI version.
--SBMLSchema L1V2, L2V1, L2V2, L2V3, L2V4, L3V1 This switch works in combination with the --exportSBML switch and determines which SBML level and version is going to be used for SBML export. Currently the following schemas are supported SBML Level 1 Version 2 (L1V2), SBML Level 2 Version 1 (L2V1), SBML Level 2 Version 2 (L2V2), SBML Level 2 Version 3 (L2V3), SBML Level 2 Version 4 (L2V4), and SBML Level 3 Version 1 (L3V1).

If no schema is given, the export creates SBML Level 2 Version 4 files.
--exportBerkeleyMadonna string value With this option you can specify a name for the Berkeley Madonna file COPASI should export. This is useful if you want to export some COPASI files to Berkeley Madonna file format in a batch job. This only makes sense for the commandline version and it will be ignored by the GUI version.
--exportC string value With this option you can specify a name for the C source file COPASI should export. This is useful if you want to export some COPASI files to C source code in a batch job. This only makes sense for the commandline version and it will be ignored by the GUI version.
--exportXPPAUT string value With this option you can specify a name for the XPPAUT file COPASI should export. This is useful if you want to export some COPASI files to XPPAUTs ODE file format in a batch job. This only makes sense for the commandline version and it will be ignored by the GUI version.
-c, --copasidir string value This specifies the directory where COPASI has been installed. It is needed to find e.g. help files. On Windows and Mac OS X this is set automatically. On Linux it has to be specified if you want to use certain features. The GUI version of COPASI will issue a warning on startup if this has not been set. The commandline version does not need this directory to be specified and therefore ignores this option.
--configdir string value This can be used to specify the directory where COPASI stores its configuration files. Normally this is called .copasi and is located in the users home directory. But if you want COPASI to use a different one, you can specify it with this switch.
--configfile string value This can be used to specify the filename where COPASI loads and stores its configuration. Normally this is called COPASI and is located in the directory specified with --configdir. But if you want COPASI to use a different filename, you can specify it with this switch.
--home string value This can be used to tell COPASI where your home directory is located. Normally you don't have to use this.
-t, --tmp string value This option can be used to specify a temporary directory where COPASI will auto-save some data periodically. Normally COPASI uses the systems temporary directory (e.g. /tmp/ under Linux).
--license With this commandline option, COPASI will print its license and exit.
--nologo This option suppresses the output of the "Logo" when CopasiSE is run. The "Logo" usually consist of the version of COPASI and some license statement.
--validate This commandline option can be used to validate the given file. The file can either be a COPASI file or an SBML file.
--verbose This commandline option tells COPASI to print more output on what it is doing to std::out.




Created by: system. Last Modification: Thursday 15 of May, 2014 09:27:46 EDT by shoops.