Skam Userguide

Chris Mungall

Skam is a makefile replacement. The main difference between skam and the make the utility is in how they handle pattern matching. Normal makefiles utilise text pattern matching, skam uses the even more powerful concept of function matching. These function constructs are known as skolem functions.

Table of Contents
I. Part1
1. Getting started
Example program
How it works
2. Skam protocol language
System parameters
Builtin targets
Module system
Looping over datasets and targetlists
Command line interface
Cleaning up
3. Execution
Status targets
Asynchronous Execution
Job submisssion
4. Storing targets in a database
Datastore wrappers
Skamdb Datastore
5. Interacting with prolog
6. Functional programming
Skam is a functional-logical programming language
7. Decision points
8. Skam for GNU/make users
II. Skam Modules
9. The fp module
Functional Programming
10. The biosequence_analysis module