diff --git a/docs/src/gettingstarted.md b/docs/src/gettingstarted.md index 32efed7..5a44eaa 100644 --- a/docs/src/gettingstarted.md +++ b/docs/src/gettingstarted.md @@ -232,14 +232,16 @@ By default, `Conda.jl` puts environments into `~/.julia/conda/envs//bi which you can get with `Conda.bin_dir()`, so in this case, you'd next want to run ```@repl -ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:biobakery) +ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:BiobakeryUtils) ``` -Note: if you need to manually edit `ENV["PATH"]` like this, +Note 1: if you need to manually edit `ENV["PATH"]` like this, you'll need to do this each time you load julia. To get around this, you can modify you shell's `$PATH` variable, or use [`direnv`](https://direnv.net) to set it on a per-directory basis. +Note 2: If following this docs you get ERROR: UndefVarError: Conda not defined` try installing and loading `Conda.jl + ## Using MetaPhlAn and HUMAnN You should now be ready to start using MetaPhlAn and HUMAnN from julia! @@ -356,4 +358,4 @@ julia> Conda.add("tbb=2020.2", env; channel="conda-forge") If your issue isn't addressed here, or you're still having problems, please [open an issue](https://github.com/BioJulia/BiobakeryUtils.jl/issues/new/choose) -or start a discussion over on [`Microbiome.jl`](https://github.com/BioJulia/Microbiome.jl/discussions/new). \ No newline at end of file +or start a discussion over on [`Microbiome.jl`](https://github.com/BioJulia/Microbiome.jl/discussions/new).