Debian eScience with myGrid and Taverna
Contents
Introduction
The term eScience (or e-Science) describes data and CPU-time intensive research that is most likely to be performed through the integration of resources throughout the Internet. Well, it may be departments in larger corporations or collaborating universities. The term is related to computational grids but today's understanding rather associates web services. The United Kingdom has invested substantial resources towards the development of an IT infrastructure for eScience applications and other countries around the globe have followed suit. The most prominent outcome is the myGrid (www.mygrid.org.uk) effort with its workflow tool Taverna (taverna.sf.net).
This page describes the effort to adopt the development of the myGrid eScience project for the Debian Linux distribution. An Alioth project (pkg-escience) aims at streamlining efforts for interested developers.
Motivation for Debian Packaging
The DebianScience special interest group describes and provides resources for scientific computing with Debian and DebianMed, a CustomDebian distribution strives to render Debian a one-stop-shop for biomedical applications which also comprises Bioinformatics. Pkg-eScience understands itself as a dedicated effort contributing its bits to the prior two. If all works out nicely, then an easier provisioning of scientific services is possible by linking Debian-based developments via web services and myGrid to the world. Conversely, all myGrid services - the focus is yet on bioinformatics but is not technically constrained to such - will be available to Debian researchers.
The package taverna is severly outdate since no attempts have yet been initiated to adapt from ant to maven as its build tool.
Installation
In order to retrieve the packages created in this project for your local Debian machine (which is suggested to run with Debian testing or Debian unstable) please add the following to /etc/apt/sources.list:
deb http://pkg-escience.alioth.debian.org/debian ./ deb-src http://pkg-escience.alioth.debian.org/debian ./
Try apt-get install taverna. To obey the Debian Free Software Guidelines (DFSG), this project aims at using Free Java environments whenever possible. However, to reduce difficulties in a first round, the packages are mostly prepared with the Sun Java DK 5.0. Since May 2006 this is distributed with the non-free section of Debian unstable. Those Packages, that were successfully built and executed with a free Java environment, have the respective field in the table below indicated in green.
Achievements
pkg-escience packages uploaded to Debian |
|||||
Package |
svn |
Comments |
Section |
||
compiles with Taverna |
main |
||||
compiles with Taverna |
main |
Work to be done
Direct adoption of upstream packages
The sources provided by the upstream developers can be installed on Debian machines without any difficulty since Linux is a common operating system among them. It is however far from being acceptable for inclusion with the Debian main distribution. For the most pragmatic adoption for Debian the direct results of the compilation of the upstream source can be taken.
Issues for compliance with DFSG and Debian Policy
- Addition of new Debian packages. A considerable number of jar files is distributed without reference to the source
- through upstream CVS
- fetched at compile time as specified in build.xml
- Preparation of Documentation
- man pages
- preparation of packages for upstream documentation
- Compatibility with Free Java Runtime Environments
Package-specific TODO list
Moved to pkg-escience/todo.
Overview on status of packages
Core packages |
|||||
Package |
apt |
svn |
Comments |
DFSG |
Version |
taverna |
x |
x |
current Taverna 1.0 CVS, apparently works |
no |
|
mygrid |
- |
- |
|
||
Otherwise missing libraries |
|||||
Package |
apt |
svn |
Comments |
DFSG |
Version |
ensj |
x |
compiles with Taverna |
no |
|
|
martj |
x |
incompatibility with Taverna |
no |
|
|
freefluo |
x |
x |
decided for wrong source |
no |
|
x |
comes with some jars, compiles with Taverna |
compiles with gcj (three trivial fixes in comments for non UDF characters), not tested |
|
||
x |
no dependencies, works with Taverna |
free Java not tested |
|
||
x |
no dependencies |
built with kaffe |
1.6.2 |
||
axis |
x |
untested |
no |
|
|
jastor |
X |
requires more recent Jena than distributed with upstream Taverna |
free Java not tested |
|
|
jena |
X |
requires more libraries, unclear compatibility with Debian libxercesImpl, compiles with jastor |
no |
|
|
arq |
X |
requires more libraries, untested |
no |
|
|
X |
no dependencies, compiles with arq |
kaffe |
20061220 |
||
jena-iri |
X |
all dependencies in Debian or here (icu4j), compiles with arq |
free Java not tested |
|
|
talisman |
- |
- |
does not compile with recent libraries (e.g. ensj), many compile time errors |
no |
|
jedit-syntax |
X |
no dependencies, requires update to cvs version |
free Java not tested |
|
|
jmol |
X |
many more dependencies, not yet tested |
free Java not tested |
|
How to contribute
- Join
- as developer on Alioth (optional)
on the mailing list
- Send patches or indicate URL with packages of interest
Guidelines for development
Moved to pkg-escience/develguide
Related projects
in the Debian community
- Science
DebianScience Wiki page
pkg-bioc Wiki page accompaning ?BioConductor and R Debian packaging project
DebianScience/Chemistry Chemistry associated packages in and soon-to-be-in Debian
Debian-Med A [CDD] (Custom Debian Distribution) for biomedical packages
pkg-grid Alioth project (appears dormant)
pkg-scicomp Alioth project on scientific computing
Java Java and Debian Wiki page
pkg-java Alioth project
and outside of Debian
MyGrid.org.uk - the upstream page
Triana - Another workflow management environment with ties to several grids