Hello, TL;DR: Qiime tutorial is directly usable with the packages in salsa for 2020.11.1, no need for anything redundant from Debian. We need to work on JavaScript to get q2-diversity into main.
I followed https://docs.qiime2.org/2021.4/tutorials/moving-pictures/ and must admit that I am impressed. This is some nice work. The command lines can be copy'n'pasted directly from that page. What surprised me a bit was that I needed about all the modules we have currently functional - it is not that there is a core functionality in the qiime package and the additional modules are just making it somewhat nicer or so - no. You have phylogeny analyses or you don't. You have diversity anlalyses or you don't. The first trouble I could spot with this very first attempt is with the q2-diversity package. This needs JavaScript, which I (not reading the README) had missed in my first package. This however is huge: npm install --no-save && \ npm run build && \ cp licenses/* dist/ npm WARN deprecated [email protected]: 🙌 Thanks for using Babel: we recommend using babel-preset-env now: please read https://babeljs.io/env to update! npm WARN deprecated [email protected]: This loader has been deprecated. Please use eslint-webpack-plugin npm WARN deprecated [email protected]: Please see https://github.com/lydell/urix#deprecated npm WARN deprecated [email protected]: Chokidar 2 will break on node v14+. Upgrade to chokidar 3 with 15x less dependencies. npm WARN deprecated [email protected]: https://github.com/lydell/resolve-url#deprecated npm WARN deprecated [email protected]: CircularJSON is in maintenance only, flatted is its successor. npm WARN deprecated [email protected]: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2. npm WARN deprecated [email protected]: The querystring API is considered Legacy. new code should use the URLSearchParams API instead. npm WARN deprecated [email protected]: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details. npm WARN deprecated [email protected]: core-js@<3.3 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js. added 640 packages, and audited 641 packages in 38s Yes. 640 packages. We likely have quite a few of them in Debian already and can somehow help npm to find them, but - ouch. No idea how you feel about this, but I somehow sense that we should not be doing this without upstream. And preferably, we sync this with JavaScript packaging for conda - otherwise, we would always have versions out of sync. So, what I have now come up with is the invocation via the Makefile that is provided that downloads what is missing. The other concern is that the tutorial provided a classifier in a file format of what was from scikit-learn IIRC that was from a newer version of what we have in the archive. They want to have their users classify that themselves in a future version, so that was not too much of my immediate concern. Best, Steffen
