Re: [MoM] snp-sites (Was: I would like to submit a package to debian-med)

[Jorge Sebastião Soares <j.s.soares@gmail.com>]

Hi Andreas, all

I am including a bit of information on what actually is a SNP on the long the decription of the snp-sites binary.

I was also thinking of adding the usage details like:

Usage: snp_sites [-mvph] [-o output_filename] <file>
This program finds snp sites from a multi fasta alignment file.
 -m        output a multi fasta alignment file (default)
 -v        output a VCF file
 -p        output a phylip file
 -o        specify an output filename
 -h        this help message
 <file>        input alignment file which can optionally be gzipped

Do you think this should be included in the long decription?

Also for the run time library package, I have written this spiel:

 Installation of the shared library of the snp-sites is done through this package.
 This library allows python bindings through the Boost python Library.

For the development library package I now have this:

 Both static libraries and header files of the snp-sites program are

 installed through this package.

What are your thoughts on this?

Regards,

Jorge

On Mon, Jan 13, 2014 at 5:09 PM, Jorge Sebastião Soares <j.s.soares@gmail.com> wrote:

Hey Andreas,

On Mon, Jan 13, 2014 at 5:04 PM, Andreas Tille <andreas@an3as.eu> wrote:

Hi Jorge,

On Mon, Jan 13, 2014 at 04:58:28PM +0000, Jorge Sebastião Soares wrote:
> >   W: snp-sites source: out-of-date-standards-version 3.9.3 (current is
> > 3.9.5)
> >
> > which is probably hidden from your sight if you do not use the latest
> > lintian
> > from Debian unstable.
>
>
> That's correct.
> I am only building against a Sid base package. My own environment is
> actually wheezy.
> I did this simply because Sid was a bit unreliable running as a VM in
> VirtualBox (I have a macintosh machine where I run my Debian VM).

While in principle unstable should work fine in a VM I have posted here
several times how to use lintian from unstable inside a stable
environment.  You should probably seek the mailing list via keywords
like

   site:lists.debian.org/debian-med lintian from unstable /etc/apt/preferences.d

(untested - feel free to ask for more hints in case this does not reveal
anything helpful)

Sascha has just filled me in on how to do this.

I will do this first thing in the morning.
Mostly for future packages.

But I will definitely have a look at the mailing list.

Regards,

Jorge