# Setting up

## Bioinformatics Tools

We are going to be using the following tools throughout the course:
- `fastqc`
- `multiqc`
- `trimmomatic`
- `bwa`
- `samtools` (version > 1.0)
- `bcftools` (version > 1.0)
- `singularity`
- `nextflow `

The easiest way to install all of the above is through [`conda`](https://conda.io/miniconda.html) as follows:

1. Download and install the latest version of miniconda:

```
curl -O -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
```

2. Add the correct channels in the conda (so that it knows where to look for packages):

```
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
```

3. Install the required tools:

```
conda install -c bioconda fastqc multiqc trimmomatic bwa samtools bcftools singularity nextflow
```

You might also want to download and install [`IGV`](https://software.broadinstitute.org/software/igv/download), as it may be useful in several visualizations.

## Base Tools

Finally, the following tools are in all likelihood already installed in most major OSs, but you should also check for them:
- `git`
- `curl`
- `gunzip`
- `java`

## R / RStudio

[R](http://www.r-project.org/) is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use [RStudio](http://www.rstudio.com/).

**Windows**
Install R by downloading and running the [correct installer file](http://cran.r-project.org/bin/windows/base/release.htm) from [CRAN](http://cran.r-project.org/index.html). Also, please install the [RStudio IDE](http://www.rstudio.com/ide/download/desktop). Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

**Linux**
You can download the binary files for your distribution from [CRAN](http://cran.r-project.org/index.html). Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the [RStudio IDE](http://www.rstudio.com/ide/download/desktop).

### Install the required packages

We will install some specific packages as well as all packages that might be needed / useful.

```
install.packages(c("tidyverse", "ggplot2", "rafalib", "caret", "ggpubr", "GGally", "ROCR", "Boruta", "party", "earth", "mlbench",  "glmnet", "e1071", "randomForest", "neuralnet"), dependencies=c("Depends", "Suggests") );
```

Also install bioconductor, and some bioconductor-related libraries.

```
source("https://bioconductor.org/biocLite.R")
BiocManager::install()
BiocManager::install("factoextra")
BiocManager::install("fpc")
BiocManager::install("knitr")
BiocManager::install("kableExtra")
BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
BiocManager::install("DiffBind")
BiocManager::install('MotifDb')
BiocManager::install('methylKit')
BiocManager::install('genomation')
BiocManager::install('ggplot2')
BiocManager::install('TxDb.Mmusculus.UCSC.mm10.knownGene')
BiocManager::install("AnnotationHub")
BiocManager::install("annotatr")
BiocManager::install("bsseq")
BiocManager::install("DSS")

```

That's it, all done! You have now all the tools in place!