Re: GMAP -- Align mRNA and EST sequences to a genome
On Mon, May 10, 2010 at 05:31:12PM -0700, Shaun Jackman wrote:
> > 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
> upstream license?
I'm quite frequently using:
Files: debian/*
License: Same as <program name>
(in case it <program has a DFSG free license). Otherwise in most cases
BSD license will fit.
> The default location can be overridden by a command line option (-D)
> or an environment variable (GMAPDB).
>
> How about /var/cache/gmap?
> http://www.pathname.com/fhs/pub/fhs-2.3.html#VARCACHEAPPLICATIONCACHEDATA
Sounds good. I'd recommend a wrapper around gmap which explicitely
makes use of this option.
> 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.
Please mind the spacing! I guess the lines with " * known" in the beginning
need an additional blank in front to make sure it is a correct itemizing.
Also last line needs a space in front.
Thanks for working on this
Andreas.
--
http://fam-tille.de
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