11_install_system_programs.Rmd

# Install system programs

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Objective: Learn how to install programs in GNU/Linux

As we have seen in the [4 unix file system](http://perso.ens-lyon.fr/laurent.modolo/unix/4_unix_file_system.html#lib-and-usrlib) session, programs are files that contain instruction for the computer to do things. Those files can be in binary or text format (with a [shebang](http://perso.ens-lyon.fr/laurent.modolo/unix/9_batch_processing.html#shebang)). Any of those files, present in a folder of the [**PATH**](http://perso.ens-lyon.fr/laurent.modolo/unix/9_batch_processing.html#path) variable are executable anywhere by the user. For system wide installation, the program files are copied within shared folder path containained in the [**PATH**](http://perso.ens-lyon.fr/laurent.modolo/unix/9_batch_processing.html#path) variable.

Developers don’t want to reinvent the wheel each time they want to write complex instruction in their programs, this is why they use shared library of pre-written complex instruction. This allows for quicker development, fewer bugs (we only have to debug the library once and use it many times), and also [better memory management](http://perso.ens-lyon.fr/laurent.modolo/unix/6_unix_processes.html#processes-tree) (we only load the library once and it can be used by different programs).

## Package Manager

However, interdependencies between programs and libraries can be a nightmare to handle manually this is why most of the time when you install a program you will use a [package manager](https://en.wikipedia.org/wiki/Package_manager). [Package manager](https://en.wikipedia.org/wiki/Package_manager) are system tools that will handle automatically all the dependencies of a program. They rely on **repositories** of programs and library which contains all the information about the trees of dependence and the corresponding files (**packages**).

System-wide installation steps:

- The user asks the package manager to install a program
- The **package manager** queries its repository lists to search for the most recent **package** version of the program (or a specific version)
- The **package manager** construct the dependency tree of the program
- The **package manager** check that the new dependency tree is compatible with every other installed program
- The **package manager** install the program **package** and all it’s dependencies **packages** in their correct version

The main difference between GNU/Linux distribution is the package manager they use

- Debian / Ubuntu: [apt](https://en.wikipedia.org/wiki/APT_(Debian))
- CentOS / RedHat: [yum](https://en.wikipedia.org/wiki/YUM_(software))
- ArchLinux: [pacman](https://en.wikipedia.org/wiki/Pacman_(Arch_Linux))
- SUSE / OpenSUSE: [zypper](https://en.wikipedia.org/wiki/Zypper)
- Gentoo: [portage](https://en.wikipedia.org/wiki/Portage_(software))
- Alpine: [apk](https://wiki.alpinelinux.org/wiki/Alpine_newbie_apk_packages)

Packages manager install the packages in **root** owned folders, you need **root** access to be able to use them.

<details><summary>Solution</summary>
<p>
```sh
docker run -it --volume /:/root/chroot alpine sh -c "chroot /root/chroot /bin/bash -c 'usermod -a -G sudo etudiant'" && su etudiant
```
</p>
</details>

### Installing R

**R** is a complex program that relies on loots of dependencies. Your current VM run on Ubuntu, so we are going to use the `apt` tool (`apt-get` is the older version of the `apt` command, `synaptic` is a graphical interface for `apt-get`)

You can check the **r-base** package dependencies on the website [packages.ubuntu.com](https://packages.ubuntu.com/focal/r-base). Not too much dependency ? Check the sub-package **r-base-core**.

You can check the **man**ual of the `apt` command to install **r-base-core**.

<details><summary>Solution</summary>
<p>
```sh
sudo apt install r-base-core
```
</p>
</details>

What is the **R** version that you installed ? Is there a newer version of **R** ?

### Adding a new repository

You can check the list of repositories that `apt` checks in the file `/etc/apt/sources.list`.

You can add the official cran repository to your repositories list:

```sh
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu <release_name>-cran40/'
```

You can use the command `lsb_release -sc` to get your **release name**.

Then you must add the public key of this repository:

```sh
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
```

### Updating the repository list

You can now use `apt` to update your repository list dans try to reinstall  **r-base-core**

<details><summary>Solution</summary>
<p>
```sh
sudo apt update
```
</p>
</details>

The command gives you a way to list all the upgradable **packages**, which version of **R** can you install now ?

You can upgrade all the upgradable **packages**.

<details><summary>Solution</summary>
<p>
```sh
sudo apt upgrade
```
</p>
</details>

With the combination of `update` and `upgrade` you can keep your whole system up to date the even the kernel files is just another package. You can use `apt` to search for the various versions of the `linux-image`.

<details><summary>Solution</summary>
<p>
```sh
sudo apt search linux-image
```
</p>
</details>



### Language specific package manager

If it’s not a good idea to have different **package manager** on the same system (they don’t know how the dependencies are handled by the other’s manager). You will also encounter language specific package manager:

- `ppm` for Perl
- `pip` for Python
- `npm` for JavaScript
- `cargo` for Rust
- `install.packages` for R
- ...

These **package managers** allows your to make installation local to the user, which is advisable to avoid any conflict with the **packages manager** of the system.

For example, you can use the following command to install `glances` system wide with `pip`

```sh
sudo pip3 install glances
```

You can now try to install `glances` with `apt`

What is the `glances` version installed with `apt`, what is the one installed with `pip` ? What is the version of the `glances` of your **PATH** ?

Next-time use `pip` with the `--user` switch.



## Manual installation

Sometimes, a specific tool that you want to use will not be available through a **package manager**. If you are lucky, you will find a **package** for your distribution. For `apt` the **package** are `.deb` files.

For example, you can download `simplenote` version 2.7.0 for your architecture [here](https://github.com/Automattic/simplenote-electron/releases/tag/v2.7.0).

<details><summary>Solution</summary>
<p>
```sh
wget https://github.com/Automattic/simplenote-electron/releases/download/v2.7.0/Simplenote-linux-2.7.0-amd64.deb
```
</p>
</details>

You can then use `apt` to install this file.

## From sources

If the program is open source, you can also [download the sources](https://github.com/Automattic/simplenote-electron/archive/v2.7.0.tar.gz) and build them.

<details><summary>Solution</summary>
<p>
```sh
wget https://github.com/Automattic/simplenote-electron/archive/v2.7.0.tar.gz
```
</p>
</details>

You can use the command `tar -xvf` to extract this archive

When you go into the `simplenote-electron-2.7.0` folder, you can see a `Makefile` this means that you can use the `make` command to build Simplenote from those files. `make` Is a tool that read recipes (`Makefiles`) to build programs.

You can try to install `node` and `npx` with `apt`. What happened ?

<details><summary>Solution</summary>
<p>
```sh
sudo apt install nodejs
```
</p>
</details>

You can use the [https://packages.ubuntu.com/](https://packages.ubuntu.com/) to search the name of the package containing the `libnss3.so` file.

<details><summary>Solution</summary>
<p>
```sh
sudo apt install libnss3                                                                                                                            
```
</p>
</details>

What now ? Installing dependencies manually is an iterative process...

<details><summary>Solution</summary>
<p>
```sh
sudo apt install libnss3 libatk1.0-dev libatk-bridge2.0-0 libgdk-pixbuf2.0-0 libgtk-3-0 libgbm1                                                                                                                                
```
</p>
</details>

Yay we should have every lib !

What now ? A nodejs dependency is missing... After, some query on the internet we can find the solution...

<details><summary>Solution</summary>
<p>
```sh
sudo apt install libnss3 libatk1.0-dev libatk-bridge2.0-0 libgdk-pixbuf2.0-0 libgtk-3-0 libgbm1
npm install --save-dev electron-window-state                                                                                                                                
```
</p>
</details>

And now you understand why program packaging takes time in a project, and why it’s important !

You can finalize the installation with the command `make install`. Usually the command to build a tool is available in the `README.md` file of the project.

Read the `README` file of the [fastp](https://github.com/OpenGene/fastp) program to see which methods of installation are available.

Installing programs and maintain different versions of a program on the same system, is a difficult task. In the next session, we will learn how to use [virtualization](./12_virtualization.html) to facilitate our job.

> We have used the following commands:
>
> - apt to install packages on Ubuntu
> - pip3 to install Python packages
> - npm to install Nodejs packages
> - make to build programs from sources