[Bio-Linux] Re: Bio-Linux

[Tony Travis]

Casey M. Finnerty, Ph. D. wrote:
> Dear Dr. Travis:
> 
> I saw your post below, and I have a question for you. I am also 
> interested in installing the Bio-Linux packages onto some machines 
> running (K)ubuntu Dapper Drake. I looked for the xlibs package you 
> mentioned and found it in the hoary repository. I also found xlibs-dev 
> in the Dapper repository. Is it possible that the latter would allow 
> Bio-Linux installation? I hesitate to install the old xlibs, as I worry 
> that it might mess up other parts of my system. (e.g., I see that xlibs 
> “Breezy” was designed to remove all the XKB configuration files in the 
> xlibs package.)

Hello, Casey.

I also found xlibs-dev in Dapper, but the bio-linux-base directories 
depended on xlibs, and xlibs-dev did not satisfy that dependency. In 
fact the xlibs from Hoary is a transitional package used to satisfy 
dependencies. It only installs these files:

/.
/usr
/usr/share
/usr/share/doc
/usr/share/doc/xlibs
/usr/share/doc/xlibs/copyright
/usr/share/doc/xlibs/changelog.Debian.gz

> If you still recommend using xlibs Hoary, please let me know if you’ve 
> experienced any problems as a result.

No, I didn't experience any problems. However, the "xlibs" dependency of 
bio-linux-base-directories package has now been removed, so I've removed 
xlibs from my 'biobuntu' system because it's no longer needed. If you 
want to know more about our 'biobuntu' project, which is part of my NBX 
(NuGO Black Box) project, please have a look at:

	http://nbx1.rri.sari.ac.uk

We've remastered the Ubuntu Dapper 6.06 LTS 'live' install CD with all 
the 'public' Bio-Linux packages pre-installed, but it does not yet have 
anything like the functionality of the NEBC 'live' DVD :-)

Our 'biobuntu' DVD is still a work in progress, and is primarily being 
developed as a way of installing pre-configured 'biobuntu' onto a hard 
disk. Although this can be done with the Knoppix-based NEBC 'live' DVD, 
the resulting Linux installation it creates is very difficult to upgrade 
because of the strange mixture of packages from different distributions 
used in Knoppix. The 'biobuntu' DVD is also intended to be used as a 
'rescue' DVD for the NBX's if they go wrong.

> Thanks!
> 
> Casey
> 
> ***********************
> Hello, Bio-Linux'ers
> 
> As part of my NuGO 'Black-Box' project, I've been comparing Ubuntu
> 'Dapper' and Debian 'Etch': One reason why I hesitated to adopt Ubuntu
> 'Dapper', initially, is that the Bio-Linux 'base-directories' package
> has a dependency on Debian 'xlibs' which is not present in Ubuntu
> 'Dapper'. This package is, however, present in Ubuntu 'Hoary', so I
> installed the 'xlibs' package from 'Hoary' into 'Dapper' and Bio-Linux
> now installs and runs OK under Ubuntu (with the sun-java packages).
> [...]

Best wishes,

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687