Seqan version in Debian (Was: Flexbar release 2.4)
[Sören, I have put you explicitly in CC because I hope you might have
some direct contact to seqan authors. Otherwise it seems I might need
to subscribe their mailing list to sort this out]
Hi,
I just noticed that our watch file does not report the latest seqan
version and thus it went a bit out of focus. When checking now I
realised that the downloadable source archive does not contain the
applications any more but just the header files. I was not able to find
the source of the applications at their web site.
My plan regarding flexbar would be: Get seqan 1.4.1 packaged first and
continue with flexbar once this is available.
Sören, could you help in clarifying the seqan issue (if not please say
so and I will try to subscribe the list).
Kind regards
Andreas.
On Sat, Aug 17, 2013 at 02:16:32PM +0100, Tony Travis wrote:
> On 30/07/13 14:25, Johannes.Roehr@mdc-berlin.de wrote:
> > Hey Tony,
>
> Hi, Johannes.
>
> Sorry about my late reply - I've been on holiday in California...
>
> [Please note my new email addrerss: I no longer work at the University
> of Edinburgh. I'm back working at the University of Aberdeen again]
>
> > yesterday I published release 2.4 of Flexbar on sourceforge. I made
> > sevaral extensions, including reading and writing compressed files,
> > support for usage of stdin (first read file) and stdout (except
> > paired reads). I also improved various statistics and simplified the
> > format option, which only has to be set in case of quality-based
> > trimming with a fastq file now. Moreover, I adapted the new SeqAn
> > 1.4.1 release.
> >
> > It should work to use SeqAn 1.4 or 1.4.1 with Flexbar. I excluded the
> > SeqAn library from the src download this time. The thought is that
> > SeqAn can be used in debian, but I saw that SeqAn 1.4 is not yet
> > available. Let me know if you prefer to have SeqAn in the src
> > download tarball as long as version 1.4 is not in debian. I could
> > exchange it with a download that includes the SeqAn library.
> >
> > Furthermore, I remarked that the argument parser provides the
> > possibility to write out the help screen in man document format,
> > which could help you to prepare man pages for debian. Today, I added
> > a hidden option (--man) to write out the help as man formatted text.
> > This feature is unfortunately not part of the new Flexbar release,
> > but can be used with a fresh checkout of the trunk version.
>
> I've CC'ed this Andreas to ask for his advice about how to proceed with
> your new upstream version. Thanks again for Flexbar, which I continue to
> find very useful!
>
> Tony.
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis@abdn.ac.uk, skype:ajtravis
>
>
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