> For the complete documentation index, see [llms.txt](https://docs.bcbi.brown.edu/codiac-for-health/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.bcbi.brown.edu/codiac-for-health/computing/julia/packages.md).

# Packages

<mark style="color:$primary;">In computer programming, a package is a collection of modules or programs that are often published as tools for a range of common use cases, such as text processing and doing math. Programmers can install these packages and take advantage of their functionality within their own code.</mark>&#x20;

This page provides instructions for installing, using, and troubleshooting packages in Julia.

## Installing Packages <a href="#installing_packages" id="installing_packages"></a>

* Start Julia REPL by typing the following in Terminal or PowerShell (Note: do not need to type $ - this is to indicate the shell prompt)

```
$ julia
```

* Go into REPL mode for Pkg, Julia’s built in package manager, by pressing `]`

```
$ julia ]
```

```
$ (@v1.4) pkg>
```

* Update package repository in Pkg REPL

```
$ (@v1.4) pkg> update
```

* Add packages in Pkg REPL

```
$ (@v1.4) pkg> add CSV
```

```
$ (@v1.4) pkg> add DataFrames
```

* Check installation

```
(@v1.4) pkg> status
            Status `~/.julia/environments/v1.0/Project.toml`
                [336ed68f] CSV v0.4.3
                [a93c6f00] DataFrames v0.17.1
                ...
```

* Get back to the Julia REPL and exit by pressing backspace or ^C.

```
(@v1.4) pkg>

julia>
```

* To see REPL history

```
$ more ~/.julia/logs/repl_history.jl
```

## Using Packages <a href="#using_packages" id="using_packages"></a>

```julia
julia> using CSV
julia> using DataFrames

julia> exit()
```

## Troubleshooting <a href="#troubleshooting" id="troubleshooting"></a>

* If you get an error like: `ERROR: SystemError: opening file "C:\\Users\\User\\.julia\\registries\\General\\Registry.toml"`: No such file or directory
  * Delete `C:\\Users\\User\\.julia\\registries` where User is your computer’s username and try again
  * <https://discourse.julialang.org/t/registry-toml-missing/24152>

## Resources <a href="#documentation" id="documentation"></a>

* [Julia Pkg](https://docs.julialang.org/en/v1/stdlib/Pkg/index.html)
* [Julia Package Registries](https://julialang.org/packages/)
* [JuliaHealth](https://juliahealth.org/) and [BioJulia](https://github.com/BioJulia) organizations (focused on Julia packages for health and life sciences)
* Julia Package: [CSV.jl](https://juliadata.github.io/CSV.jl/stable/)
* Julia Package: [DataFrames.jl](https://juliadata.github.io/DataFrames.jl/stable/)


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