| | 2 | |
| | 3 | The main goal of our model is to unambiguously specify a bioinformatics workflow execution in a distributed compu- tational environment. The model includes the entire workflow specification and specifications for individual workflow tasks. Hence, we divide our model into two structural layers or interfaces. These are a job interface to specify the work- flow and tool interface to specify an individual workflow task. These interfaces are used in two main framework use scenarios: |
| | 4 | |
| | 5 | * specifying a workflow or job for execution, and |
| | 6 | * adding a new tool to the framework tool repository. |
| | 7 | |
| | 8 | Hence, analyses provided by the tool can be included |
| | 9 | into workflows. Let us examine these models in more detail. The tool |
| | 10 | model is similar to the [http://main.g2.bx.psu.edu/ Galaxy] tool file, where a tool is described as a set of operations, which it can perform. A tool operation can participate in workflow execution. Our platform is aimed to support specifying any external analysis tool, which can be invoked from a command line or be run as an executable script (e.g. a shell or R-script). In contrast with the Galaxy description, we do not have complex operation parameters in the model. Instead, we treat an operation with differ- ent parameters as a set of separate operations. A list of tool operations grows depending on the complexity of the operations parameterisation. Still, the specification of an individual operation remains simple. |
