[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: Imported io-lib, a Staden library

On 8 Jul 2008, at 1:13 pm, Andreas Tille wrote:

IMHO we are not in a hurry with this.  But I want to use this chance
to ping our fellow Debian developers at Sanger to consider some cooperation with the internal Debian project that really targets at their application.

In principle, I'm more than happy to help out, but as with everything else, my time is limited. I'm responsible for all central software maintenance at Sanger, so it sort of comes under my remit (I maintain our internal Debian package repository, for example) but the contents of that repository are not generally bio packages, they're local backports from lenny, or perl packages built with dh-make-perl to support other applications. The reasons there's no biomed in there are:

1) Frequently, different groups in the Institute want different versions of the same program to be available, which is hard if we use packaged versions. Exonerate (which I see you've already packaged) is a very bad example of this... in Ensembl's internal software directory there are no less than seven different versions of it. Plus, since its author Guy is a user of the system, there are frequently test development versions which appear and disappear.

2) Using packages suddenly makes it my job (as a sysadmin) to update the software on the machines when required. On the other hand, giving each group an NFS-mounted software directory to which they have write access means that individual groups can install and support whichever version they want, whenever they want, and I only have to maintain the development tools they require.

He, guys please have another look at the project and perhaps visit


What I can do to help, if not packaging directly, is act as a liaison with the people actually developing the stuff you want. For example, I know the authors of both SSAHA and Artemis quite well. I've been periodically asking Zemin to alter SSAHA2 so that it can be made DFSG- compliant, and he agrees in principle, it's just a case of his group actually finding the time to do it. I'll ping him again about it.


The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
Reply to: