Re: report on first qiime tutorial with Debian packages
On 8/13/21 11:46 PM, Steffen Möller wrote: > > On 12.08.21 20:12, Steffen Möller wrote: >>> BTW, q2-diversity (Build-+)Depends on q2-emperor which again depends on >>> python3-emperor which are not in the archive. And both do not look ready >>> for upload yet (in interim state) >>> If you make them ready, let me know. >> I'll have a look. My immediate questions are answered: Debian can >> perform the compute and create output files. Since this was running >> remotely, I admittedly have not yet checked if emperor (which provides >> an interactive 3D visualisation in your web browser) is truly functional. > > I had that look, both at emperor and q2-emperor. > > emperor fails the reprotest > https://salsa.debian.org/med-team/emperor/-/jobs/1805122/artifacts/browse/debian/output > but that report did not ring any immediate bells. Because it injects timestamps in the documentation. This is due to jsdoc package itself, see here[1] I think the fix will be similar to this[2] But I definitely do not have the time to fix it there and test, maybe I'll just file a bug report with this hint and someone from reproducible-builds team will take that up [1]: https://salsa.debian.org/georgesk/jsdoc-toolkit/-/blob/master/jsdoc-toolkit/templates/jsdoc/allfiles.tmpl#L53 [2]: https://salsa.debian.org/js-team/node-d3/-/blob/master/debian/patches/reproducible-builds.patch Nilesh OpenPGP_signature Description: OpenPGP digital signature
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: -- 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
Re: report on first qiime tutorial with Debian packages
On 12.08.21 20:12, Steffen Möller wrote: BTW, q2-diversity (Build-+)Depends on q2-emperor which again depends on python3-emperor which are not in the archive. And both do not look ready for upload yet (in interim state) If you make them ready, let me know. I'll have a look. My immediate questions are answered: Debian can perform the compute and create output files. Since this was running remotely, I admittedly have not yet checked if emperor (which provides an interactive 3D visualisation in your web browser) is truly functional. I had that look, both at emperor and q2-emperor. emperor fails the reprotest https://salsa.debian.org/med-team/emperor/-/jobs/1805122/artifacts/browse/debian/output but that report did not ring any immediate bells. Best, Steffen
