We will not introduce you to some advanced concepts of TOPP, which will increase your productivity and easy usage.

Global database for search engine adapters

In your $HOME directory you will find an OpenMS.ini file in the .OpenMS subfolder. This INI file contains global parameters which are honored by many/all TOPP tools - depending on what the parameters refer to. The id_db_dir parameter allows you to specify one or more directories where you have placed FASTA files (or related, e.g., .psq files). If you now specify just a filename (without path) in an ID engine adapter, the filename 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 you to build scripts and/or TOPPAS pipelines which are portable across several computers - you just have to adapt the OpenMS.ini once on each machine.

Note when using TOPPAS: You can 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 you to name a non-existing file. After you've selected the file, you can however edit the filename and remove the path (this will issue a warning which you can ignore).

Note: This approach does not work for our MascotAdapters, as each Mascot instance has its own database managed internally. You can however, make sure that the database is present on all mascot servers you are going to use, thus making the INI settings portable.

Using External tools in your workflows

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

See also: share/OpenMS/TOOLS/EXTERNAL/ReadMe.txt for details.