diff --git a/docs/src/index.md b/docs/src/index.md index bd90322..a75c70d 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -3,7 +3,9 @@ *TreeKnit* is a julia package that performs inference of reassortment events in segmented genomes, such as human influenza. Additionally, it can reconstruct Ancestral Reassortment Graphs for segment pairs. ## Installation -You can simply install *TreeKnit* using the julia package manager (if you don't have julia, you can get it from [here](https://julialang.org/downloads/)): +*TreeKnit* requires Julia version 1.7, it may not work with higher or lower versions. You can get v1.7.3 of Julia [here](https://julialang.org/downloads/oldreleases/#:~:text=v1.7.3). Alternatively, you can install julia 1.7.3 into a conda environment. + +You can install *TreeKnit* using the julia package manager: ```julia using Pkg Pkg.add("TreeKnit") diff --git a/src/cli.jl b/src/cli.jl index 632c90e..b85a2bd 100644 --- a/src/cli.jl +++ b/src/cli.jl @@ -33,7 +33,7 @@ We suggest two sets of defaults for running TreeKnit. `--better-trees` will prod - `-v, --verbose`: set verbosity to 1 - `--auspice-view`: return ouput files for auspice """ -@main function treeknit( +Comonicon.@main function treeknit( nwk_file1::AbstractString, nwk_file2::AbstractString, nwk_files::AbstractString...; # options outdir::AbstractString = "treeknit_results",