Re: [MoM] deepnano getting info from maintainer

[Afif Elghraoui]

Hello,

على الأربعاء 16 تشرين الثاني 2016 ‫01:50، كتب Çağrı ULAŞ:
> 
> I finally find fast5 files from poretools which is an utility for
> converting fast5 to fasta/fastq file. There are fast5 examples on
> poretools' github page. Is there any thing we need to specify for this
> data in debian directory?

I created the poretools Debian package, but the data files are not part
of any binary package. Do you two think it would be a good idea to make
a poretools-data package? Then you could build-depend on it to get
access to these files.

Çağrı, perhaps you can see whether those files are useful for you. If
they are, we can arrange to get them packaged and you can pull it in as
a dependency.

regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: [MoM] deepnano getting info from maintainer

[Çağrı ULAŞ]

Hi Andreas,

I finally find fast5 files from poretools which is an utility for
converting fast5 to fasta/fastq file. There are fast5 examples on
poretools' github page. Is there any thing we need to specify for this data
in debian directory?

Regards

2016-11-12 1:01 GMT+03:00 Andreas Tille :

> Hi,
>
> On Fri, Nov 11, 2016 at 08:34:15PM +0200, Çağrı ULAŞ wrote:
> > Working on autopkgtest but I have issues with deepnano. There are no man
> > pages or example files I found.
>
> Did you tried -h/--help options that might be used with help2man?
>
> > Only bitbucket page have a basic usage but
> > this is more different from classic alignment tools.
>
> If there is no chance with help2man you might try to find some simple
> introduction how to write manpages (or check out a simple manpage on the
> Debian system) and feed in the content of the bitbucket page.
>
> > I try to run with some
> > .npz datas in nets_data directory. But give me an error 'Unable to open
> > file (File signature not found)'. Anyway, .npz datas are numpy's
> > uncompressed files according to scipy's docs. 'OMP_NUM_THREADS=1
> > deepnano_basecall' command uses fast5 files. Cant get any fast5 file.
> Where
> > can I get them, any ideas?
>
>  * Asking upstream
>  * Asking Canberk how he found example files
>  * Hoping for hints of other readers here
>
> Sorry, I can not help myself since I'm not working as bioinformatican.
>
> > Nowadays, lots of work on me at university but I'll try to communicate
> more
> > often.
>
> OK.
>
> Kind regards
>
>   Andreas.
>
> --
> http://fam-tille.de
>
>


-- 
*Çağrı ULAŞ*
about.me/cagriulas

Re: Help needed to package manta which needs samtools >= 1.2 and libbam.a

[Andreas Tille]

On Wed, Nov 16, 2016 at 08:41:10AM +0100, Olivier Sallou wrote:
> 
> don't know how, but if it needs libbam.a, this means you are in static build, 
> not using shared libraries, which is not the way Debian does.
> So it seems you should tweak the make recipes to build with shared libraries 
> instead of static compilation. this will solve your issue and use our .so 
> files.

Sure - but we do not have any package providing libbam.so.
A libbam is only provided by legacy samtools package.

Kind regards

   Andreas.

-- 
http://fam-tille.de