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 * Compatibility with Free Java Runtime Environments, currently the Sun SDK 1.5 is used from DebianUnofficial (www.debian-unofficial.org)  * Compatibility with Free Java Runtime Environments

Debian eScience with myGrid and Taverna

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

bytecode

pkg-escience

compiles with Taverna

main

biojava

svn

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

svn

compiles with Taverna

no

martj

x

svn

incompatibility with Taverna

no

freefluo

x

x

decided for wrong source

no

uddi4j

x

svn

comes with some jars, compiles with Taverna

compiles with gcj (three trivial fixes in comments for non UDF characters), not tested

icu4j

x

svn

no dependencies, works with Taverna

free Java not tested

wsdl4j

x

svn

no dependencies

built with kaffe

1.6.2

axis

x

svn

untested

no

jastor

X

svn

requires more recent Jena than distributed with upstream Taverna

free Java not tested

jena

X

svn

requires more libraries, unclear compatibility with Debian libxercesImpl, compiles with jastor

no

arq

X

svn

requires more libraries, untested

no

json

X

svn

no dependencies, compiles with arq

kaffe

20061220

jena-iri

X

svn

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

svn

no dependencies, requires update to cvs version

free Java not tested

jmol

X

svn

many more dependencies, not yet tested

free Java not tested

How to contribute

  • Join
  • Send patches or indicate URL with packages of interest

Guidelines for development

Moved to pkg-escience/develguide

in the Debian community

and outside of Debian


CategoryJava