Hi,
I'm writing you on behalf of the Debian Med team that has the goal to
package free software of the field of biology and medicine for official
Debian. Since we want to upgrade QIIME to version 1.9.1 we also need
to package sumatry which I just announced (see below).
The packaging is nearly finished but there is a remaining issue. The
manual sumatra_user_manual.pdf is only available as PDF. In Debian a
PDF without source (LaTeX, etc.) is considered as binary without source
and can not be distributed. Would you mind to add the source of the PDF
manual to the release tarball. As an intermediate solution any place to
download the source would be fine.
BTW, I have tried to convert the output of sumatra into a manpage:
https://anonscm.debian.org/viewvc/debian-med/trunk/packages/sumatra/trunk/debian/sumatra.1?view=markup
Feel free to take this over into your distribution.
Since it might be that we also will package sumaclust: Also here we
would need the source for the PDF.
BTW, while in sumatra download tarball 1.0.01 both tools were included
in one download tarball, a split was done in 1.0.03. From my naive
point of view the split of these tools would rectify a higher increase
of the version number and also some documentation file (say NEWS) would
help the user to realise what happened.
Kind regards
Andreas.
On Wed, Aug 05, 2015 at 09:41:20PM +0200, Andreas Tille wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Andreas Tille <tille@debian.org>
>
> * Package name : sumatra
> Version : 1.0.03
> Upstream Author : Tiayyba Riaz e.a
> * URL : http://metabarcoding.org/sumatra
> * License : CeCILL-2
> Programming Lang: C
> Description : fast and exact comparison and clustering of sequences
> With the development of next-generation sequencing, efficient tools are
> needed to handle millions of sequences in reasonable amounts of time.
> Sumatra is a program developed by the LECA. Sumatra aims to compare
> sequences in a way that is fast and exact at the same time. This tool
> has been developed to be adapted to the type of data generated by DNA
> metabarcoding, i.e. entirely sequenced, short markers. Sumatra computes
> the pairwise alignment scores from one dataset or between two datasets,
> with the possibility to specify a similarity threshold under which pairs
> of sequences that have a lower similarity are not reported. The output
> can then go through a classification process with programs such as MCL
> or MOTHUR.
>
>
> Remark: This package was prepared by Tim Booth for BioLinux as a
> predependency for QIIME 1.9.1. It is taken over by Debian Med and
> maintained at
> svn://anonscm.debian.org/debian-med/trunk/packages/sumatra/trunk/
>
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>
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