Re: 3 new packages

[Andreas Tille <tillea@rki.de>]

On Fri, 25 Mar 2005, Nelson A. de Oliveira wrote:

> gff2aplot: Pair-wise alignment-plots for genomic sequences in PostScript.
> Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html
> License: GNU GPL
> Package: http://biolinux.df.ibilce.unesp.br/naoliv/med/gff2aplot/
Just uploaded.

> gff2ps: Produces PostScript graphical output from GFF-files.
> Homepage: http://genome.imim.es/software/gfftools/GFF2PS.html
> License: GNU GPL
> Package: http://biolinux.df.ibilce.unesp.br/naoliv/med/gff2ps/
It depends from bash 3.0.  Is this dependency really necessary.
I'm just asking because I guess it will keep the package outside
Sarge (if it should have any chance which is quite low anyway.

> raster3d: set of tools for generating high quality raster images of
> proteins or other molecules.
> Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html
> License: None. Can be distributed(?)
> Package: http://biolinux.df.ibilce.unesp.br/naoliv/med/raster3d/
I just did an 'fmt -s' on the debian/copyright file to adjust
line lengthes for easiere reading.

> The big problem here is Raster3D. I have put it on non-free section. Could someone take a look at him ans say if it can go on Debian? Info is available at debian/copyright file.
IMHO it can go into non-free.

> Also, could someone verify the quality of the packages, if they are OK?
I think gff2aplot is fine, thus it is uploaded.  I personally have
no bash 3.0 installed thus I was not yet able to verify gff2ps.  I have
to admit that I never have seen a shell script program with 3602 lines
of code in one file.  Normally this kind of complex programming should
be done more modular and probably not really in in bash code which
depends from a certain bash version.  This sounds a little bit suspicious
to me.  But if it would work and people regard it as nice tool then
this is no argument to keep it outside.

Regarding to raster3d I would suggest to split up the package into
an architecture dependant package and a common package bacause the
size of the architecture independant part is about ten times of the
architecture dependant binaries.

Kind regards

         Andreas.

--
http://fam-tille.de

This package was debianized by Nelson A. de Oliveira <naoliv@gmail.com> on
Fri, 25 Mar 2005 17:06:13 -0300.

It was downloaded from http://www.bmsc.washington.edu/raster3d/

Upstream Author:

Originally written by David J. Bacon and Wayne F. Anderson; extensions,
revisions, modifications, ancillary programs by Mark Israel,
Stephen Samuel, Michael Murphy, Albert Berghuis, and Ethan A Merritt
<merritt@u.washington.edu> - Department of Biochemistry & Biomolecular
Structure Center - University of Washington, Seattle

Copyright:
There is no explicit licence for Raster3D, but Ethan allowed to distribute
it with the following restritions: Raster3D can't be sold.

From the author of Raster3D:

It is fine to use Raster3D for commercial purposes;
in fact you can see from the covers of many scientific journals that it is
used for this by many publishers.  Raster3D may not be sold, however.

As I told you, I have explicitly given Debian permission to include
Raster3D in the past, but it never seems to emerge from the other
end of the process.

CITING THE PROGRAM
If you use the package to prepare figures for publication, please give
proper credit to the authors; the proper citation for the most recent
version of the package is Merritt & Bacon (1997) as given below.

REFERENCES
Bacon, D.J., & Anderson, W.F. (1988) ``A Fast Algorithm for
Rendering Space-Filling Molecule Pictures''. (abstract of paper
presented at the Seventh Annual Meeting of the Molecular Graphics
Society). J. Molec. Graphics 6, 219-220.
Kraulis, P.J. (1991) ``MOLSCRIPT: a program to produce both detailed
and schematic plots of protein structures''. J. Appl. Cryst. 24, 946-950.
Merritt, E.A. & Murphy, M.E.P. (1994) ``Raster3D Version 2.0 - A Program
for Photorealistic Molecular Graphics''. Acta Cryst. D50, 869-873.
Merritt, E.A. & Bacon, D.J. (1997) ``Raster3D Photorealistic Molecular
Graphics''. Methods in Enzymology 277, 505-524.