Debian eScience with myGrid and Taverna

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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 [http://www.mygrid.org.uk myGrid] (www.mygrid.org.uk) effort with its workflow tool [http://taverna.sf.net Taverna] ([http://taverna.sf.net 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 ([http://alioth.debian.org/projects/pkg-escience/ pkg-escience]) has just been created.

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 [http://en.wikipedia.org/wiki/Bioinformatics bioinformatics] but is not technically constrained to such - will be avaiable to Debian researchers.

The package taverna is useful now since one does not require to set up any local services to join Grid use and development.

Installation

In order to retrieve the packages created in this project for your local Debian machine (which is suggested to run testing or 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. At the moment, all packages are prepared with the Sun Java DK 5.0. Since May 2006 this is distributed with the non-free section of Debian unstable.

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

Package-specific TODO list

Moved to ["pkg-escience/todo"].

Overview on status of packages

Core packages

Package

apt

svn

Comments

DFSG

taverna

x

x

current Taverna 1.0 CVS, apparently works

no

mygrid

-

-

Otherwise missing libraries

Package

apt

svn

Comments

DFSG

ensj

x

[http://svn.debian.org/wsvn/pkg-escience/ensj/trunk/ svn]

compiles with Taverna

no

martj

x

[http://svn.debian.org/wsvn/pkg-escience/martj/trunk/ svn]

incompatibility with Taverna

no

biojava

x

[http://svn.debian.org/wsvn/pkg-escience/biojava/trunk/ svn]

compiles with Taverna

almost

bytecode

x

[http://svn.debian.org/wsvn/pkg-escience/bytecode/trunk/ svn]

compiles with Taverna

almost

freefluo

x

x

decided for wrong source

no

uddi4j

x

[http://svn.debian.org/wsvn/pkg-escience/uddi4j/trunk/ svn]

comes with some jars, compiles with Taverna

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

icu4j

x

[http://svn.debian.org/wsvn/pkg-escience/icu4j/trunk/ svn]

no dependencies, works with Taverna

free Java not tested

wsdl4j

x

[http://svn.debian.org/wsvn/pkg-escience/wsdl4j/trunk/ svn]

no dependencies, compiles with axis

free Java not tested

axis

x

[http://svn.debian.org/wsvn/pkg-escience/axis/trunk/ svn]

untested

no

jastor

X

[http://svn.debian.org/wsvn/pkg-escience/jastor/trunk/ svn]

requires more recent Jena than distributed with upstream Taverna

free Java not tested

jena

X

[http://svn.debian.org/wsvn/pkg-escience/jena/trunk/ svn]

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

no

arq

X

[http://svn.debian.org/wsvn/pkg-escience/arq/trunk/ svn]

requires more libraries, untested

no

json

X

[http://svn.debian.org/wsvn/pkg-escience/json/trunk/ svn]

no dependencies, compiles with arq

free Java not tested

jena-iri

X

[http://svn.debian.org/wsvn/pkg-escience/jena-iri/trunk/ 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

[http://svn.debian.org/wsvn/pkg-escience/jedit-syntax/trunk/ svn]

no dependencies, requires update to cvs version

free Java not tested

jmol

X

[http://svn.debian.org/wsvn/pkg-escience/jmol/trunk/ svn]

many more dependencies, not yet tested

free Java not tested

How to contribute

Guidelines for development

Moved to ["pkg-escience/develguide"]

in the Debian community

and outside of Debian


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