Debian package with a script auto-running a qiime2-tutorial
Hello,
You may recall my positive news about the Qiime2 tutorial that I could
run - except for a final step that was affected by version
incompatibility of scikit-learn with a binary file that was meant to
feed a classifier. To run this far, I needed about all the q2-modules
that we have currently in salsa. Hence, it felt natural to use the same
commands as a test script for our qiime2 packages. But - how? As part of
the qiime2 package or the q2cli? Or get the q2cwl into the distribution
and transform the tutorials' workflows into formal workflows?
I now created a qiime-tutorial package [1] that offers a script to
execute all the commands presented in the "moving pictures" tutorial
[2]. The other tutorials I would then add once we have updated the qiime
packages to its latest release. This first tutorial downloads about
25MByte of data when executed. That is not too bad, I thought. When I
started this, I eventually ran into a failure and had difficulties to
identify the script that caused the problem. I hence converted the
script to a Makefile, so repeated executions are not performing anything
redundant. The problem was caused by the dada2 R package that now
reproducibly crashes, but a closer look suggests a missing dist package
in demux. It has not crashed before I installed various updates in
unstable. But that is exactly why this script could be useful.
The repository in [1] is prepared to build as a Debian package. I am
still somewhat uncertain about how to best automate the testing. And if
the "package" should truly hide in a community/tutorials subgroup I am
uncertain about, too.
Let this be a start.
Best,
Steffen
[1] https://salsa.debian.org/med-team/community/tutorials/qiime-tutorials
[2] https://docs.qiime2.org/2021.4/tutorials/
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