Re: bcbio - kind of ready, but dependencies gffutils and pybedtools are no longer distributed

[Steffen Möller <steffen_moeller@gmx.de>]

I now updated pybedtools to 0.8.0.

bcbio also builds with that newer version.

4 tests of the many pybedtools fail, one of them about internet access, 
but also one that looks like an error. Could someone please have a look? 
I'll upload with tests disabled in the meantime.

Best,

Steffen

On 17.01.19 16:59, Michael Crusoe wrote:
> Glad to hear about the BCBIO progress!
>
> I removed those packages, they were only removed due to lack of use, 
> so it is not problem if you bring them back.
>
> În joi, 17 ian. 2019 la 17:53, Steffen Möller <steffen_moeller@gmx.de 
> <mailto:steffen_moeller@gmx.de>> a scris:
>
>     Hello,
>
>     I just finished what started at 2018 Sprint, i.e. the packaging of
>     bcbio. Their december release builds without a patch and autotests
>     with
>     Python 3 are fine. I just uploaded 1.1.2 to salsa - please have a
>     look.
>     Now, running pbuilder I ran into missing packages for
>
>     https://tracker.debian.org/pkg/python-pybedtools
>     https://tracker.debian.org/pkg/python-gffutils
>
>     which in the meantime have been removed from the distribution. The
>     source tree of bcbio makes strong direct use of them both. Can we
>     have
>     them back? There was no technical reason for these packages to
>     disappear, right?
>
>     Best,
>
>     Steffen
>
>
>
>
> --
> Michael R. Crusoe
> Co-founder & Lead, Common Workflow Language project 
> <http://www.commonwl.org/>
> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
> https://orcid.org/0000-0002-2961-9670 
> <https://impactstory.org/u/0000-0002-2961-9670>
> mrc@commonwl.org <mailto:mrc@commonwl.org>
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