Re: q2-diversity tests Re: report on first qiime tutorial with Debian packages
Hi Tony,
On 12.08.21 20:34, Tony Travis wrote:
On 12/08/2021 19:16, Steffen Möller wrote:
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Ran 153 tests in 557.862s
Hi, Steffen.
QIIME/QIIME2 are notoriously sensitive to the versions of supporting
programs
Thank you for pointing this out. I admit to be impressed by qiime2, and
or some reason that does not make me worry too much. We have a
respective reference result file provided with the tutorials and can
thus ensure that a) everything runs and b) we get equivalent results. If
there are notable differences between the results then this is a bug -
in one of the libraries or in qiime2.
so I think it is important to validate your packaging of QIIME2
against the same analysis using the upstream-supported Bioconda package.
The results files of the tutorials are offered online. I suggest we
implement packages with the code that are contributing to the tutorials
and run them. Then everyone can compare if any deviation is critical or
interesting.
Quite a few packages are outdated in Debian that are used in qiime. So,
this likely means that we will be updating them and then be newer than
what qiime was using when the tutorials were created. I hence do not
strive for binary identity. The overall trends should be the same, though.
I've taught QIIME2 using Jupyter Notebooks on Cyverse:
https://cyverse-jupyter-qiime2.readthedocs-hosted.com/en/latest/README.html
This was well received by the course participants in comparison to
when they were just using the CLI.
I had a look at https://cyverse.org and it seems very compatible with
what Debian is after, but I have not fully grasped it all, yet. Thank
you for this pointer (and your work).
My plan for "after the tutorial packages are functional" is to prepare
decent descriptions of the packages, i.e. the text in the debian/control
files for each package. Should you (or anyone reading this) find(s) the
leisure to help out with that, this would be much appreciated. I made a
first attempt at
https://salsa.debian.org/med-team/q2-diversity/-/blob/master/debian/control
which felt o.k.-ish while I was writing it, yesterday, but today reads a
bit weird :o)
Best,
Steffen
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