# How to install applications

There are four different methods to get your favorite application installed on Bioinformatics Center's servers. The three first options doesn't require system administrator privileges and can be carried out by user.

## Download binaries

You can always download already compiled binaries from Internet. All you need to do is extract downloaded archive file (e.g. *.gz, *.zip) files to any directory (e.g. $HOME/bin/). Please make sure that the binaries have been compiled for appropriate platform e.g. "linux 64-bit", "linux x64". 

## Download source code and compile

Always ready-made binaries are not available or you need to recompile application from the source code again. In this case download the source code to the server, extract source code and follow installation instructions. Normally you will find compilation and installation instructions from among the downloaded files (search for README or INSTALLATION files). The most often you just need to do something like this:

```
tar xzf APPLICATION.tar.gz # extract source code
cd APPLICATION # move into the source code directory
./configure # generate makefiles before compilation
make # compile application
```

## Use conda and configure Bioconda channel

Follow instructions from [[https://bioconda.github.io/user/install.html#install-conda|Bioconda]]. In short this procedure requires Miniconda installation, channels configuration and application installation.

**The first install Miniconda** 

```
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
```

**The second set up channels**
After installing conda you will need to add the bioconda channel as well as the other channels bioconda depends on. It is important to add them in this order so that the priority is set correctly (that is, conda-forge is highest priority).

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

**The third install packages**
Any packages from any configured channels can be installed into the current conda environment:
```
conda search bwa
conda install bwa
```

Or create a new environment and install packages:

```
conda create -n aligners bwa 
```

## Request system wide install

If you prefer to have system wide installation of you favorite application you need to send software installation request to bioinformatics@uef.fi. The system wide installation requires system administrator privileges.