Re: GMAP -- Align mRNA and EST sequences to a genome
On 10 May 2010 23:32, Andreas Tille <andreas@an3as.eu> wrote:
> 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.
I'll use the BSD license.
Files: debian/*
Copyright: 2010 Shaun Jackman <sjackman@debian.org>
License: BSD
See `/usr/share/common-licenses/BSD'.
>> 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'll configure gmap at compile time for the default DB directory to be
/var/cache/gmap:
override_dh_auto_configure:
dh_auto_configure -- --with-gmapdb=/var/cache/gmap
>> 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.
Noted.
> Thanks for working on this
No problem at all. Thanks for the help!
Cheers,
Shaun
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