Debian eScience with myGrid and Taverna
?TableOfContents(3)
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
- 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, currently the Sun SDK 1.5 is used from ?DebianUnofficial (www.debian-unofficial.org)
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 |
compiles with Taverna |
no |
|
martj |
x |
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 |
comes with some jars, compiles with Taverna |
compiles with gcj (three trivial fixes in comments for non UDF characters), not tested |
|
icu4j |
x |
no dependencies, works with Taverna |
free Java not tested |
|
wsdl4j |
x |
no dependencies, compiles with axis |
free Java not tested |
|
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 |
|
json |
X |
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 |
many more dependencies, not yet tested |
free Java not tested |
How to contribute
- Join
- as developer on Alioth (optional)
on the [http://lists.alioth.debian.org/mailman/listinfo/pkg-escience-devel 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
[http://alioth.debian.org/projects/pkg-emboss/ pkg-emboss] Alioth project (dormant, sadly)
- ["BOINC"]
[?DebianScienceChemistry] Chemistry associated packages in and soon-to-be-in Debian
[http://www.debian.org/devel/debian-med/ Debian-Med] A [CDD] (Custom Debian Distribution) for biomedical packages
[https://alioth.debian.org/projects/pkg-grid/ pkg-grid] Alioth project (appears dormant)
[https://alioth.debian.org/projects/pkg-scicomp/ pkg-scicomp] Alioth project on scientific computing
- ["Java"] Java and Debian Wiki page
[http://www.debian.org/doc/manuals/debian-java-faq/ Debian Java FAQ]
[http://pkg-java.alioth.debian.org/ pkg-java] Alioth project
[http://pkg-java.alioth.debian.org/building.html Java packaging hints]
[http://lists.alioth.debian.org/mailman/listinfo/pkg-java-maintainers Mailing list]
and outside of Debian
[http://www.mygrid.org.uk ?MyGrid.org.uk] - the upstream page
[http://www.vl-e.com/ Virtual Laboratory for e-Science]
[http://www.trianacode.org/ Triana] - Another workflow management environment with ties to several grids