Institute of Bioinformatics Münster
TinT - Command Line Version


To run the command line version first the archive must be downloaded here and executed in a terminal with
java [-Xmx512m] -jar tintcmd.jar [-conf filename] [-in filename-or-http] [-out filename] [-type b|c|d|m] [-size size] [-check cr1|sine]
The parameter -Xmx is not neccessary and sets the memory maximum for the java environment (in this case to 512MB). If the application hangs while processing data, it could be neccessary to encrease this parameter.

Error Messages

Error messages are written (added) into a file called tintcmd.log in the folder $HOME/.bioinf (on unix machines) or the appropriate folder .bioinf in your user's directory in Windows. In case of failure please send this file along with a failure description.

Configuration File

In addition to the (default) configuration file of the graphical application, the command line version has 2 new sections and 5 additional parameters to specify input, the type and destination of output and transpositions of interest. The first 5 parameters may be overwritten by the command line parameters -input, -output, -type, -size and -check.

[Tran Selection]
  • in: a local filename or a http address where the input data can be obtained.
  • out: a local filename where the output data will be written.
  • type: the type of output. It may only specified one of the following values: [b]ar graph, [c]umulative graph, [d]istribution graph, [m]atrix
  • size: the size of the generated graphics, width "x" height size (like 1000x1000).
  • check: the method to calulate the insertions ("cr1" or "sine").
  • [Tran Selection] specifies the transposition names of interest. If this section is ommitted all transposition names read from the input file are taken to be selected. Otherwise the input file is evaluated against the names given in this section.
Note: If filenames and http addresses contain blanks, you have to enclose the address or the filename in inverted commas!
2015-05-06 08:44