TOPP for Advanced Users#

This tutorials has some advanced concepts of TOPP, which will increase productivity and easy usage.

Global database for search engine adapters#

In your $HOME directory find an OpenMS.ini in the .OpenMS subfolder. This INI file contains global parameters which are used by many/all TOPP tools, depending on what the parameters refer to. The id_db_dir parameter allows to specify one or more directories where FASTA files (or related, e.g., .psq files) are placed. Specified filename (without path) in an ID engine adapter, will be looked up in the current working directory. If its not found, the directories specified in id_db_dir will be searched. This allows to build scripts and/or TOPPAS pipelines which are portable across several computers, just adapt the OpenMS.ini once on each machine.

Tip

When using TOPPAS: Use an “input file” node to specify the FASTA file for several engines simultaneously. However, when selecting the file, TOPPAS will use the absolute pathname and the dialog will not allow to name a non-existing file. After selecting the file you can however edit the filename and remove the path (this will issue a warning which can be ignored).

Note

This approach does not work for OpenMS MascotAdapters, as each Mascot instance has its own database managed internally. Make sure that the database is present on all mascot servers you’re going to use, thus making the INI settings portable.

Using external tools in workflows#

OpenMS supports the wrapping of external tools (like msconvert from ProteoWizard), thus allowing to build scripts and/or TOPPAS pipelines containing external tools.