Re: About FASTX-Toolkit and its possible redistribution in Debian.

[Andreas Tille <andreas@an3as.eu>]

Hi,

any comments on this.  You did not give a contact e-mail address
and Gordon might have missed your mail in case he is not subscribed to
our mailing list.  At least I will add the programs to our prospective
package list.

Kind regards

      Andreas.

On Mon, Jun 29, 2009 at 01:25:43PM +0900, Charles Plessy wrote:
> Le Fri, Jun 26, 2009 at 04:32:58PM -0400, Assaf Gordon a écrit :
> >
> > I converted libgtextutils to shared library, and made fastx-toolkit use it.
> >
> > What's next ?
> >
> >> http://lists.debian.org/debian-med/
> >
> > I've joined the list.
> 
> Dear Gordon,
> 
> I continue the discussion on the list since I am not too familiar with C
> libraries.
> 
> To summarise for the other readers, you developed three utilities for
> ???next-generation sequencing??? fastx-toolkit, column_normalizer and crosstab
> that use one library, gtextutils, that you recently converted from static to
> shared library to facilitate its packaging and the packaging of the tools in
> Debian.
> 
> http://hannonlab.cshl.edu/fastx_toolkit
> http://hannonlab.cshl.edu/column_normalizer/
> http://hannonlab.cshl.edu/crosstab/
> 
> Their source code is managed in a mercurial repository. Is it publically
> available?
> 
> Since you proposed to do the packaging by yourself (thanks !) the Debian source
> package (materialised by a ???debian??? directory in the sources) can be managed at
> your convenience, either in your the mercurial repository itself together with
> the sources, or alone in our subversion directory. Both choices will produce
> identical source (.dsc) and binary (.deb) packages in the Debian archive,
> so it is a matter of taste. Maybe starting from within the hg repository
> is the simplest to begin with.
> 
> Debian source packages consist in the original upstream archive (*.orig.tar.gz)
> and the debian directory provided as a patch (*.diff.gz), plus some meta-data
> and md5 sums (*.dsc). For this reason, if the debian directory is managed in
> the mercurial repository, I recommend that the original sources you release to
> the public do not contain the debian directory (it can collide with the
> .diff.gz file).
> 
> Now for the library packaging:
> 
> > I found online a recommendation for libtool libraries to use the  
> > CURRENT:REVISION:AGE standard.
> >
> > That's fine, I used 4:0:0.
> >
> > But where do the header files go ?
> >
> > is it to /usr/include/gtextutils-4.0.0/
> > or /usr/include/gtextutils
> > or something else ?
> 
> Unless we want to maintain two different versions of gtextutils side-to-side
> (and we really would like to avoid that), I think that the headers can go to an
> unversioned directory. The development package itself does not have a version
> number in its name, so there is only one version in Debian to build against at
> a given time.
> 
> Have a nice day,
> 
> -- 
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
> 
> 
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