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/
