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.
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**).
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 managers](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:
Systemwide 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 **package manager** install the program **package** and all its dependencies **packages** in their correct version
The main difference between GNU/Linux distribution is the package manager they use
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@@ -71,7 +71,7 @@ docker run -it --volume /:/root/chroot alpine sh -c "chroot /root/chroot /bin/ba
## 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`)
**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**.
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- `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.
These **package managers** allow you 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`
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.
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 ?
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@@ -258,5 +258,5 @@ Read the `README` file of the [fastp](https://github.com/OpenGene/fastp) program
> - make to build programs from sources
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.
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 add an vitual IDE periferic storage on which we can boot on
We add a virtual IDE peripheric storage on which we can boot on.
```sh
VBoxManage storagectl Ubuntu20.04 --name IDE --add ide --controller PIIX4 --bootable on
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@@ -138,7 +138,7 @@ You can use the `systemctl` command and the `/` key to search for this daemon.
Like VirtualBox, you can install system programs within a container.
Prebuilt container can be found on different sources like [the docker hub](https://hub.docker.com/) or [the biocontainers registry](https://biocontainers.pro/registry).
Prebuilt containers can be found on different sources like [the docker hub](https://hub.docker.com/) or [the biocontainers registry](https://biocontainers.pro/registry).
