[JOSS REVIEW] Installation instructions

[tkchafin]

Are the installation instructions correct? I can't get installation to work without first manually installing dada2 and phyloseq

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("dada2")
BiocManager::install("phyloseq")

[adrientaudiere]

You are right. I tried on a docker image, and we effectively needed this code before. I saw no direct solution for the moment. In a discussion on stackoverflow they suggest using BiocManager::install(MiscMetabar), but until MiscMetabar is only available on GitHub, there is no obvious solution. I plan to submit MiscMetabar to CRAN during the next summer.

I updated the README file to better explain the installation. Thanks for the time you spent on my submission.

[tkchafin]

Sounds good, that's all I had intended as the fix, just to make sure the documentation was accurate

[iimog]

After merging the pr #43, these instructions are no longer required in the README:

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("dada2")
BiocManager::install("phyloseq")

It does not hurt to run these commands beforehand, it's just not necessary anymore.