Getting Started With Julia, notes for bioinformaticians

I recently started working with Julia, Below are some initial notes that I have been taking while installing and working with the programming language as well as the advantages that it can provide.

I tried to install originally on macintosh but found that it failed immediately. I was able to run the command to install juliaup however.

Finally the most important part is that you want to be able to use the following command


curl -fsSL https://install.julialang.org | sh

Then you can install a new julia version with the following command. Where 1.10 is the software version of the Julia language.


juliaup add +1.10

This will add a “channel” where the channel you will pick from the latest versions that are available for julia. Currently as of this writing the versions are 1.10 as the stable release version.

https://github.com/jupyter-lsp/jupyterlab-lsp install jupyterlab LSP

Which Development Environment to use

can use pluto VS code is the only one that has julia insider for viewing dataframes The vs code plugin can get setup exactly almost the same as Rstudio with a few complaints and not as indepth for analysis Julia packages

Useful functional packages

transducers folds

But most of the main things are similar still hard to beat R studio for all of its integration that it has.

Using Package compiler!

For compilation need to use Pkg.instantiate() and Pkg.resolve()

first need to activate a julia project start the package manager and do

activate .

Go up a directory then activate then rerun package compiler and get it to work Then you will have the dependencies correctly listed

https://bkamins.github.io/julialang/2020/05/10/julia-project-environments.html

Julia has made a breaking change in the types instead of using void the type is now “nothing”

make sure to include this when you are running the code.

Transducers and automa for quickly parsing files are also available

https://docs.juliahub.com/General/FiniteStateTransducers/stable/ if you care about weighted finite state transducers

How do I rbind in julia?

want to make a dataframe from a list of vectors

Using vcat fpr rbinding matrices, or hcat for cbinding matrices. Once you have the matrix worked out then you can easily turn this into a dataframe.

VIM Plugin

I use chad nvim and found there were a few things to be aware of because of the lazy package installation.

to get vim stuff working for inserting hte unicode symbols you need to do a ton of stuff that will take a lot of time https://github.com/folke/lazy.nvim/blob/c734d941b47312baafe3e0429a5fecd25da95f5f/README.md#L104

you need to only load it when ft is true

  {
    "JuliaEditorSupport/julia-vim",
    ft=".jl",
    config=true
  },

in your package spec change lazy to a different boolean it won’t work and install when you use lazy loading and it will automatically detect the filetype for you anyway lazy boolean?

https://docs.julialang.org/en/v1/manual/unicode-input/