If you need a HiPerGator account, follow the instructions on the lab-wiki: https://github.com/weecology/lab-wiki/wiki/Programming:-HiPerGator-Intro-Guide
Log onto HiPerGator (substituting your username for
Follow the installation instructions for Python on HiPerGator. No need to actually install packages yet.
Create a file named .Rprofile to allow for local installs (substituting your username for
R, install the core Python retriever (yes, this happens in
R, which is kind of magical).
If you get an error that the conda environment
'r-reticulate' does not exist, you may need to create it first. Run the following lines and then retry the
conda_install('r-reticulate', 'retriever') command:
If you get an error about “HTTP error 404” and “Rate limit remaing”, you may need to setup a GITHUB_PAT key on HiPerGator - https://happygitwithr.com/github-pat.html
MATSS::install_retriever_data("veg-plots-sdl", force_install = TRUE)
If you receive an error about the number of arguments, e.g.
Error in py_call_impl(callable, dots$args, dots$keywords) : TypeError: install_csv() takes from 1 to 4 positional arguments but 5 were given
then you will need a newer version of retriever than was previously installed.
Exit R to return to the command line, and then use the following commands to install retriever from github:
Then, retry the command at the beginning of this step in R.
MATSSpipeline on HiPerGator you will need to setup
draketo use slurm for parallel scheduling. See https://github.com/weecology/MATSS-LDATS/ for an example of how to do this.