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Basic Setup
There are many different ways that people use Yoshimi, and more than a few varieties of approaches to setup. On this page we outline just a few of many thoughts we and others are using.
The most significant distinction, is probably using ALSA more or less alone, as diverging from the use of JACK.
ALSA is by far the most inclusive and best-supported audio and MIDI driver set for Linux. Yoshimi will connect to it directly if told to do so from the command line, using -A and -a (uppercase for audio, lower case for MIDI).
JACK is a process which runs in the background as an connective, so that multiple hardware devices and software tools can deliver and receive audio and MIDI data to and from each other. By using JACK we can incorporate many different tools in a flowing multi-dimensional chain, with amazing flexibility the marvelous result.
JACK Audio Connection Kit at the Arch Linux wiki
What is JACK within Ubuntu's official documentation
Debian 6 Installing JACK2, on the Rivendell Wiki
For quite a while, if you ran JACK and needed it to be dependable, you either did a lot of command-line fancy work or used a GUI tool called QJackCTL. There are more options now, but this method does remain, and many use it; and it can be a very good idea to start using JACK here, and then branch out, having learned the basis of the others. One very capable among us has been using JACK and Yoshimi and other tools for quite a while, and he does his preliminary initialization with QJackCTL, runs his Yoshimi instance(s) separately, and then fires up Rosegarden, which completes his JACK connectives during its startup. There are quite a few other tools now which can do JACK connectives as part of their functionality; two among many are qtractor and Carla. It is also very possible to do much with automation, for instance to produce a fully self-starting musical instrument.