The ruffus module has the following design goals:
- Simplicity. Can be picked up in 10 minutes
- Elegance
- Lightweight
- Unintrusive
- Flexible/Powerful
Automatic support for
- Managing dependencies
- Parallel jobs
- Re-starting from arbitrary points, especially after errors
- Display of the pipeline as a flowchart
- Reporting
To be written
Tools used to build executables can be used to manage computational pipelines. These include
- GNU make
- scons
- ant
It is often necessary to learn a specialised (domain-specific) language. GNU make syntax, for example, is much criticised because of limited support for abstraction compared with modern programming languages like C, Perl, python etc. GNU makefiles can quickly become unmaintainable.
Pipeline specifications are usually written in a “declarative” rather than “imperative” manner. You write a specification that describes the dependencies, and the tool figures out how to perform the computations in the correct order. However, because GNU make and its kin depend entirely on file dependencies, the links between pipeline stages can be difficult to trace, and nigh impossible to debug when there are problems.
There are also complete workload managements systems such as Condor. Various bioinformatics pipelines are also available, including that used by the leading genome annotation website Ensembl, Pegasys, GPIPE, Taverna, Wildfire, MOWserv, Triana, Cyrille2 etc. These all are either hardwired to specific databases, and tasks, or have steep learning curves for both the scientist/developer and the IT system administrators
See also
Make like tools
See also
Bioinformatics pipelines
- Condor:
- http://www.cs.wisc.edu/condor/description.html
- Ensembl Analysis pipeline:
- http://www.ncbi.nlm.nih.gov/pubmed/15123589
- Pegasys:
- http://www.ncbi.nlm.nih.gov/pubmed/15096276
- GPIPE:
- http://www.biomedcentral.com/pubmed/15096276
- Taverna:
- http://www.ncbi.nlm.nih.gov/pubmed/15201187
- Wildfire:
- http://www.biomedcentral.com/pubmed/15788106
- MOWserv:
- http://www.biomedcentral.com/pubmed/16257987
- Triana:
- http://dx.doi.org/10.1007/s10723-005-9007-3
- Cyrille2:
- http://www.biomedcentral.com/1471-2105/9/96
Bruce Eckel’s insightful article on A Decorator Based Build System was the obvious inspiration for the use of decorators in Ruffus.
- The rest of the Ruffus takes uses a different approach. In particular:
Ruffus uses task-based not file-based dependencies
Ruffus tries to have minimal impact on the functions it decorates.
Bruce Eckel’s design wraps functions in “rule” objects.
Ruffus tasks are added as attributes of the functions which can be still be called normally. This is how Ruffus decorators can be layered in any order onto the same task.
Languages like c++ and Java would probably use a “mixin” approach. Python’s easy support for reflection and function references, as well as the necessity of marshalling over process boundaries, dictated the internal architecture of Ruffus.
The Boost Graph library for text book implementations of directed graph traversals.
Graphviz. Just works. Wonderful.