Re: IBDA for Debian
Hi again,
meanwhile I think I found what I needed at
https://code.google.com/p/hku-idba/downloads/list
but some clarification about the difference between
idba-1.1.1.tar.gz IDBA all in one package 1.1.1 (IDBA, IDBA-UD, IDBA-Hybrid and IDBA-Tran)
idba_tran-1.0.13.tar.gz IDBA-Tran: A low-expression sensitive de novo Iterative de Bruijn Graph Assembler for Transcriptome
idba_hybrid-1.0.12.tar.gz IDBA-Hybrid: an iterative De Bruijn Graph De Novo Assembler for hybrid sequencing
idba_ud-1.0.9.tar.gz IDBA-UD: An Assembler for short read sequencing data with highly uneven sequencing depth
might be interestesting. I also noticed that despite the same version
number is used some files in the ngopt svn repository are more recent.
Thanks for any clarification
Andreas.
On Thu, Feb 13, 2014 at 01:46:08PM +0100, Andreas Tille wrote:
> Hi Yu Peng,
>
> I'm writing you on behalf of the Debian Med project. Or aim is to
> include all Free Software which is useful in medicine and biology into
> official Debian. Here you can see a list of the current packages
> available in Debian in the field of Biology[1] which migh be relevant
> for you.
>
> I stumbled upon ngopt[2] which fits perfectly into our scope and I would
> like to package this for Debian as well. Wenn havin a look into its
> source code repository I have detected ibda which somehow looks like a
> third party project which is simply included. The Debian philosphy is
> following a modular concept and thus we would like to fetch this code
> from its main source. Unfortunately I have not found the source at some
> other place like inside the ngopt SVN. There are even two directories:
>
> http://code.google.com/p/ngopt/source/browse/#svn%2Fvendor%2FIDBA%253Fstate%253Dclosed
>
> and
>
> http://code.google.com/p/ngopt/source/browse/#svn%2Ftrunk%2Fidba-1.1.1
>
> while the later is featuring the latest version number.
>
> Could you please clarify the role of idba and where we can find the
> latest source code for Debian packaging?
>
> Kind regards and thanks for providing idba as Free Software
>
> Andreas.
>
> [1] http://blends.debian.org/med/tasks/bio
> [2] http://code.google.com/p/ngopt/
>
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