Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas,

sorry for the delay in replying. I did get your last two emails but it seems the fist one (On Mon, Jul 25, 2016 at 09:45:57PM) never arrived.

Thanks so much for the suggestions. Tin, can you take a look at these two sets of suggestions and update the source code of MetaPhlAn2 accordingly?

some small fixes: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch?view=markup
some spelling issues https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/debian/patches/spelling.patch?view=markup

Tin can also provide more info about the binary data in db_v20. The files ending with "bt2" are created using a script in the Bowtie2 package (bowtie2-build) using a sequence file Tin can provide (it can also be recovered from the bt2 files with bowtie2-inspect if I remember well).

For the mpa_v20_m200.pkl Tin can also provide the uncompressed python object (or he can provide a couple of lines of code to uncompress it?)

For the LEfSe package I just added the license in the bitbucket repository. For the description, I think you can use the following page:

https://bitbucket.org/biobakery/biobakery/wiki/lefse

Does it sound like an appropriate description for the package?

Let me know if you have other questions or if I missed answering to other emails.

thanks so much for your work!

Nicola

On Sat, Jul 30, 2016 at 10:47 PM Andreas Tille <andreas@an3as.eu> wrote:

Hi Nicola,

did you received the two mails about licensing (+ in the case of lefse
a description) ?

Kind regards

Andreas.

On Wed, Jul 27, 2016 at 09:09:01AM +0200, Andreas Tille wrote:
> Hi again,
>
> I have another question in addition to the one below. I was packaging
> MetaPhLan2 to make use of it in my final target package for metaBIT[1]
> which in addition is using some Python code I've found here
>
> https://bitbucket.org/nsegata/lefse
>
> This code has neither any description I could use for the package nor a
> license. It would be really great if you could provide a basic
> description and for packaging a free license would be needed.
>
> Kind regards
>
> Andreas.
>
> On Mon, Jul 25, 2016 at 09:45:57PM +0200, Andreas Tille wrote:
> > Hi Nicola,
> >
> > we just had some conversation about pyphlan. I now want to package
> > MetaPhLan2 for Debian and I have prepared the needed packaging stuff.
> > I did some small fixes
> >
> > https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch?view=markup
> >
> > and fixed some spelling issues
> >
> > https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/debian/patches/spelling.patch?view=markup
> >
> > you might possibly want to take over in your upstream source.
> >
> > For the final upload to Debian I would need some information how the
> > binary data files in db_v20 were created. Debian requires somehow
> > editable source for each file. This is probably not possible for the
> > files in question but we need to provide some information where the
> > files are obtained from.
> >
> > Kind regards
> >
> > Andreas.
>
> [1] https://bitbucket.org/Glouvel/metabit/wiki/
>
> --
> http://fam-tille.de

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