TOPP

How to disable the OpenMS update check.
Starting with OpenMS 2.1 all TOPP tools will check for updated versions of the tools online and will print an information message if a newer version is available. This version check occurs only once per day and tool. Information on which tools are executed will be collected anonymously to identify which tools are no longer used and to optimally distribute development resources. If the feature causes problems or concerns, it can be disabled by setting the environment variable 'OPENMS_DISABLE_UPDATE_CHECK' to "ON".
How can I change the temporary directory that OpenMS uses?
By default OpenMS will use the system wide temporary directory (defined either by TMPDIR, TEMP or the TMP environmental variable, depending on your Operating System). You can override this by setting the environmental variable OPENMS_TMPDIR.
Calling msConvert (of ProteoWizard) results in small mzML files with no peak data.
The Thermo interface expects an English locale setting. Otherwise it will silently forget to return peak data. Set your locale to English and it should work.
Some TOPP tools always crashes when executed. Other TOPP tools work properly.
If a error message similar to
OpenMS::File::find(...) of File.cpp error message: the file 'CHEMISTRY/unimod.xml' could not be found

OpenMS::File::find
static String find(const String &filename, StringList directories=StringList())
Looks up the location of the file filename.

is shown, you have probably moved your OpenMS installation manually?! Then the TOPP tools cannot find some required data files anymore, e.g. XML schema files or chemical isotope data.

To fix, set the environment variable OPENMS_DATA_PATH to your <OpenMS>/share/OpenMS/ folder.
A TOPP tool crashes when loading a certain input file. Other files work properly.
If an XML input file is used, please check if the file is valid.

For most XML data formats, this can be done using the FileInfo tool. Here is how to invoke it on the commandline:
FileInfo -v -in <file>

You can also check for corrupt data in peak files:
FileInfo -c -in <file>

You can, of course, also run it via your workflow system of choice.