# Installation

## Requirements and dependencies

The rnaends package is fully developed in R (>= 4.4.2) and only relies on CRAN or BioConductor packages.


### Installation of required packages manually

Install the following packages from CRAN (with their minimum version) with your preferred installation method:

* remotes >= 2.5.0
* ggupset >= 0.4.0
* tidyverse >= 2.0.0
* VGAM >= 1.1-9

Typically, this would lead to: 
```
install.packages("remotes")
install.packages(c("ggupset", "tidyverse", "VGAM", "BiocManager"))
```

Install the following packages from BioConductor:

* DSS >= 2.54.0
* Rbowtie >= 1.46.0
* Rsamtools >= 2.22.0
* Rsubread >= 2.20.0
* ShortRead >= 1.64.0
* survcomp >= 1.56.0

Typically:
```
BiocManager::install("DSS")
BiocManager::install("Rbowtie")
BiocManager::install("Rsamtools")
BiocManager::install("Rsubread")
BiocManager::install("ShortRead")
BiocManager::install("survcomp")
```

Then, install `rnaends`:
```
remotes::install_gitlab("rnaends/rnaends")
```

**Note:** It has been tested on a fresh install of R (4.4.2) and RStudio on Windows 11 without any environment.

See de [DESCRIPTION](../DESCRIPTION) file for version details.

### Installation of required packages with an environment manager (conda or mamba)

We recommend the use of [mamba](https://mamba.readthedocs.io) (or conda) environment to ensure proper execution of all the features.

Download the environment exported file: https://gitlab.com/rnaends/rnaends/-/raw/main/rnaends.conda.env.txt

Then, use conda or mamba to re-create it:
```
mamba env create --name rnaends --file rnaends.conda.env.txt
```

Then, use it (after activation):
```
mamba activate rnaends
# then use R or Rstudio
rstudio
```

Then proceed with the following section to install the package from GitLab.



## Install from GitLab repository

The installation should work *seemlessly* by running the following command in R, but depending on your setup, conflicts can occur and it might be necessary to follow the steps of previous sections (manual install or through conda/mamba environment manager).

From the R console, use the `install_gitlab` function from the `remotes` package.
```
if (!require("remotes", quietly = TRUE))
    install.packages("remotes")

remotes::install_gitlab("rnaends/rnaends")
```

# Source code

Complete source code is available at [https://gitlab.com/rnaends/rnaends](https://gitlab.com/rnaends/rnaends).

A local copy can be downloaded with `git`:
```
git clone https://gitlab.com/rnaends/rnaends.git
```