[Debian-med-packaging] Bug#580277: GMAP -- Align mRNA and EST sequences to a genome

Charles Plessy plessy at debian.org
Wed May 5 04:01:20 UTC 2010

Le Tue, May 04, 2010 at 06:30:26PM -0700, Shaun Jackman a écrit :
> I've packaged GMAP:
> Align mRNA and EST sequences to a genome
>  GMAP: Genomic Mapping and Alignment Program
>  GSNAP: Genomic Short-read Nucleotide Alignment Program
> The ITP is here:
> http://bugs.debian.org/580277
> The git repository is here:
> git://git.debian.org/git/debian-med/gmap.git
> http://git.debian.org/?p=debian-med/gmap.git

Dear Shaun,

thank you very much for helping us to stay up to date in the field of
next-generation sequencing. Just out of curiosity, will you use the
package yourself, or did you prepare it for a friend or a colleague?

I had a look at your package and have the following comments:

 - It is non-free:

   ‘Distribution of this Package as part of a commercial software product requires
    prior arrangement with the Developers.’

   I updated debian/control accordingly. Since this license is not compatible with
   the GPL, I recommend that you chose another license for your packaging work, in
   order to avoid headaches in the future.

 - We will have to be careful when doing modifications.

   ‘Distribution of a modified version of this Package requires prior
    arrangement with the Developers.’

   I am not sure of what it means for the manpages you wrote. If you have written them
   using the output of the programs as a template, they are a derivative of them,
   and the above may mean that we need agreement of the upstream developpers before
   redistributing them. But anyway, manpages are better to be forwarded upstream. Have
   you contacted them?

 - Location of the databases.

   I have seen ‘-DGMAPDB=\"/usr/share/gmap\"’ in the build logs. Does that mean that the
   users will have to install their databases there, or is there a way to override
   this path? In general, I think Debian users expect /usr/share to be completely under
   the control of the packaging system. Perhaps another path would be better?

 - How to cite gmap.

   I am preparing a system to transfer bibliographic information from the
   packages VCS to the Ultimate Debian Database, so that sites like our web
   sentinel can easily include this information. It is not finished yet, but you
   can find more information here: http://wiki.debian.org/UpstreamMetadata   

 - Package description. How about this one:

Description: spliced and SNP-tolerant alignment programs for mRNA and short reads
 This package contains the GMAP and GSMAP programs to align biological
 sequences, and additional utilities to manage genome databases in GMAP/GSNAP
 format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
 cDNAs (complementary DNA) to reference genomes. GSNAP (Genomic Short-read
 Nucleotide Alignment Program) is a tool for aligning single and paired-end
 sequence reads as short as 14 nt and of arbitrarily long length. It can do de
 novo discovery of splice sites (including interchromosomal splicing) or use a
 datbase of known splice sites. It also tolerates known single nucleotide
 polymorphisms (SNPs) and can align bisulfite-treated DNA.

  Maybe it would be good to propose to the authors to proofread this description,
  so that we are sure that I did not under- or over-estimate the possibilities
  of their programs.

Have a nice day,

Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan

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