Qiime2 for PrecisionFDA

[AYK]

Hi, I am looking to run data using Qiime2 through PrecisionFDA.
However, I need to insult Qiime2 “as an app” in PrecisionFDA.
Can someone help with installing Qiime2 in PrecisionFDA? Is there Qiime2 code that I/ we can use?
Thank you

[ChrisKeefe]

Hi @AYK,
As long as you maintain compliance with the relevant software licenses, you’re welcome to install QIIME 2 as a PrecisionFDA app (managing licensenses in PrecisionFDA). Unfortunately, the QIIME 2 development team isn’t able to support app creation directly at this time. The platform seems to have good tutorials for creating apps, and the QIIME 2 source code is publicly available on github.

Please note that QIIME 2 uses a plugin model, and all of its bioinformatics knowledge is contained in plugins, rather than in a single centralized codebase. This gives QIIME 2 a ton of flexibility and allows it to keep up with cutting-edge methods, but may make building up an app more complex.

If you’re looking for community support or collaborators on this, feel free to post in the Other Bioinformatics Tools or Developer Discussion categories of this forum.

Here are some notes/references that may be of use:

1. PrecisionFDA’s tutorial on managing licenses
2. q2cwl generates CWL tools from QIIME 2 actions, and may be of use alongside the PrecisionFDA app import tooling discussed in their docs. NOTE: q2cwl is still a work in progress
3. A native linux installation is what you want for successful dependency management for a PrecisionFDA QIIME 2 app

Good luck!
Chris