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Re: New qiime version

Hi Steffen,

On Wed, 12 Jun 2019 at 14:44, Steffen Möller <steffen_moeller@gmx.de> wrote:
On 12.06.19 09:00, Andreas Tille wrote:

> Hi Liubov,
> On Tue, Jun 11, 2019 at 11:26:47PM +0200, Liubov Chuprikova wrote:
>> I have updated qiime for a new version 2019.4.0, which is actually the same
>> I need to use for testing newly packaged plugins. Could you please check it
>> for me and upload?
> Done.  Thanks for your work on this

Indeed. Many thanks! 
I had not thought about it much, but Qiime is a workflow that is
complete and that Debian covers in toto with all DFSG requirements in
place. It is hence something we could run repetitively on external data
to ensure the reliability of the Debian Med package tree. Opinions?
strategic aim IMHO is to make this CI work look nice to the biological
mind. The code executing the test would then be easily reproducible and
educational around the globe.

I am not familiar with how these workflow CI tests would be organized. After finishing with all the plugins, I am thinking of writing an autopkgtest that will cover all/most of the functionality of QIIME 2. BTW, their paper [1] has some worked examples as supplementary material. Hope, it will be useful.

I guess that to make these workflow CI tests attractive to a biological mind and to serve as educational, they should also be organized as documented pipelines. Do you think, there are other ways to make them reachable and reusable for a non-developer?


Steffen (still stuck somewhere within bcbio)

With regards,

[1] https://peerj.com/preprints/27295/ 

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