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

[Charles Plessy <plessy@debian.org>]

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