[Debian-med-packaging] Bug#580277: GMAP -- Align mRNA and EST sequences to a genome
sjackman at gmail.com
Tue May 11 00:31:12 UTC 2010
On 4 May 2010 21:01, Charles Plessy <plessy at debian.org> wrote:
> 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:
>> The git repository is here:
> 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.
Can you recommend a license that is DFSG free and compatible with the
> - 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?
I'm in contact with the upstream author, but not yet regarding the
Debian package. I'll forward the man pages upstream.
> - 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?
The default location can be overridden by a command line option (-D)
or an environment variable (GMAPDB).
How about /var/cache/gmap?
> - 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.
I edited and reformatted your description. How's this look?
Description: spliced and SNP-tolerant alignment for mRNA and short reads
This package contains the programs GMAP and GSNAP as well as
utilities to manage genome databases in GMAP/GSNAP format.
GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
EST, mRNA and cDNA sequences.
GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
aligning single and paired-end transcriptome reads.
Both tools can use a database of
* known splice sites and identify novel splice sites.
* known single nucleotide polymorphisms (SNPs).
GSNAP 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.
I believe these claims are correct, but of course it wouldn't hurt to check.
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