Skip to content
Snippets Groups Projects
Verified Commit d699debe authored by Laurent Modolo's avatar Laurent Modolo
Browse files

fix typo in session 3 to 5

parent e206b067
No related branches found
No related tags found
No related merge requests found
Pipeline #473 passed
Stage: deploy
    Hide whitespace changes
    Inline Side-by-side
    3_first_steps_in_a_terminal.Rmd
    + 8
    − 8
    View file @ d699debe
    ......@@ -23,11 +23,11 @@ library(fontawesome)
    knitr::opts_chunk$set(echo = TRUE)
    knitr::opts_chunk$set(comment = NA)
    klippy::klippy(
    position = c('top', 'right'),
    position = c("top", "right"),
    color = "white",
    tooltip_message = 'Click to copy',
    tooltip_success = 'Copied !')
    tooltip_message = "Click to copy",
    tooltip_success = "Copied !"
    )
    ```
    <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">
    ......@@ -158,7 +158,7 @@ What happens when you type `cd` without any argument ?
    What is the location shown in your prompt ? Is it coherent with the `pwd` information ? Can you `cd` to the `pwd` path ?
    When we move around a file system, we often want to see what is in a given folde. We want to **l**i**s**t the directory content. Go back to the `/home` directory and use to the `ls` command see how many have a home directory there.
    When we move around a file system, we often want to see what is in a given folder. We want to **l**i**s**t the directory content. Go back to the `/home` directory and use to the `ls` command see how many people have a home directory there.
    We will see various options for the `ls` command, throughout this course. Try the `-a` option.
    ......@@ -168,9 +168,9 @@ ls -a
    What changed compared to the `ls` command without this option ?
    Go to your home folder with the bare `cd` command and run the `ls -a` command again. The `-a` option makes the `ls` command list hidden files and folders. On Unix systems, hidden files and folders are all files and folders whose name starts with a "**.**".
    Go to your home folder with the bare `cd` command and run the `ls -a` command again. The `-a` option makes the `ls` command list hidden files and folders. On Unix systems, hidden files and folders are all files and folders whose name starts with a `.`.
    Can you `cd` to "**.**" ?
    Can you `cd` to `.` ?
    ```sh
    cd .
    ......@@ -178,7 +178,7 @@ cd .
    What happened ?
    Can you cd to "**..**" ?
    Can you cd to `..` ?
    ```sh
    cd ..
    ......
    4_unix_file_system.Rmd
    + 28
    − 28
    View file @ d699debe
    ......@@ -23,11 +23,11 @@ library(fontawesome)
    knitr::opts_chunk$set(echo = TRUE)
    knitr::opts_chunk$set(comment = NA)
    klippy::klippy(
    position = c('top', 'right'),
    position = c("top", "right"),
    color = "white",
    tooltip_message = 'Click to copy',
    tooltip_success = 'Copied !')
    tooltip_message = "Click to copy",
    tooltip_success = "Copied !"
    )
    ```
    <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">
    ......@@ -58,19 +58,19 @@ This file system is organized as a tree. As you have seen, every folder has a pa
    Every file can be accessed by an **absolute path** starting at the root. Your user home folder can be accessed with the path `/home/etudiant/`. Go to your user home folder.
    We can also access file with a **relative path**, using the special folder "**..**". From your home folder, go to the *ubuntu* user home folder without passing by the root (we will see use of the "**.**" folder later).
    We can also access files with a **relative path**, using the special folder `..`. From your home folder, go to the *ubuntu* user home folder without passing by the root (we will see use of the `.` folder later).
    # File Types
    As you may have guessed, every file type is not the same. We have already seen that common file and folder are different. Here are the list of file types:
    As you may have guessed, every file type is not the same. We have already seen that common file and folder are different. Here is the list of file types:
    - **-** common files
    - **d** folders
    - **l** links
    - **b** disk
    - **c** special files
    - **s** socket
    - **p** named pipes
    - `-` common files
    - `d` folders
    - `l` links
    - `b` disk
    - `c` special files
    - `s` socket
    - `p` named pipes
    To see the file type you can type the command
    ......@@ -78,11 +78,11 @@ To see the file type you can type the command
    ls -la
    ```
    The first column will tell you the type of the file (here we have only the type "**-**" and "**d**" ). We will come back on the other information later. An other less used command to get fine technical information on a file is the command `stat [file_name]`. Can you get the same information as `ls -la` with `stat` ?
    The first column will tell you the type of the file (here we have only the type `-` and `d`). We will come back on the other information later. Another less used command to get fine technical information on a file is the command `stat [file_name]`. Can you get the same information as `ls -la` with `stat` ?
    # Common Structure
    From the root of the system (**/**), most of the Unix-like distribution will share the same folder arborescence. On macOS, the names will be different because when you sell the most advanced system in the world you need to rename things, with more advanced names.
    From the root of the system (`/`), most of the Unix-like distribution will share the same folder tree structure. On macOS, the names will be different because when you sell the most advanced system in the world you need to rename things, with more advanced names.
    ## `/home`
    ......@@ -92,7 +92,7 @@ You already know this one. You will find all your file and your configuration fi
    You can find the Linux kernel and the boot manager there. What is the name of your boot manager (process by elimination) ?
    You can see a new type of file here, the type "**l**". What it the version of the **vmlinuz** kernel ?
    You can see a new type of file here, the type `l`. What it the version of the **vmlinuz** kernel ?
    ## `/root`
    ......@@ -102,17 +102,17 @@ The home directory of the super user, also called root (we will go back on him l
    The folder containing the programs used by the system and its users. Programs are simple file readable by a computer, these files are often in **bin**ary format which means that it’s extremely difficult for a human to read them.
    What is the difference between **/bin** and **/usr/bin** ?
    What is the difference between `/bin` and `/usr/bin` ?
    **/sbin** stand for system binary. What are the names of the programs to power off and restart your system ?
    `/sbin` stand for system binary. What are the names of the programs to power off and restart your system ?
    **/opt** is where you will find the installation of non-conventional programs (if you don’t follow [the guide of good practice of the LBMC](http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/ressources/good_practice_LBMC), you can put your bioinformatics tools with crapy installation procedure there).
    `/opt` is where you will find the installation of non-conventional programs (if you don’t follow [the guide of good practice of the LBMC](http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/ressources/good_practice_LBMC), you can put your bioinformatics tools with crapy installation procedure there).
    ## `/lib` and `/usr/lib`
    Those folder contains system libraries. Libraries are a collection of pieces of codes usable by programs.
    What is the difference between **/lib** and **/usr/lib**.
    What is the difference between `/lib` and `/usr/lib`.
    Search information on the `/lib/gnupg` library on the net.
    ......@@ -126,7 +126,7 @@ Contains every peripheric
    What is the type of the file `stdout` (you will have to follow the links)?
    With the command `ls -l` can you identify files of type "**b**" ?
    With the command `ls -l` can you identify files of type `b` ?
    Using `less` can you visualize the content of the file `urandom` ? What about the file `random` ?
    ......@@ -146,7 +146,7 @@ You can navigate the file with the navigation arrows. Which group the user `ubun
    To close the `less` you can press `Q`. Try the opposite of `less`, what are the differences ?
    What is the type of the file `autofs.fifo-var-autofs-ifb` in the `run` folder ? From **fifo** in the name, can you guess the function of the "**p**" file ?
    What is the type of the file `autofs.fifo-var-autofs-ifb` in the `run` folder ? From **fifo** in the name, can you guess the function of the `p` file ?
    There are few examples of the last type of file in the `run` folder, in which color the command `ls -l` color them ?
    ......@@ -176,7 +176,7 @@ stat /var/run
    What is the kind of link for `/var/run` ?
    Most of the time, when you are going to work with links, you will work with this kind of link. You can create a **l**i**n**k with the command `ln` and the option `-s` for **s**ymbolic.
    Most of the time, when you are going to work with links, you will work with this kind of link. You can create a **l**i**n**k with the command `ln` and the option `-s` for a **s**ymbolic.
    The first argument after the option of the `ln` command is the target of the link, the second argument is the link itself:
    ......@@ -212,7 +212,7 @@ ln .bashrc bashrc_linkb
    Use `stat` to also study `bashrc_linka` and `bashrc_linkb`.
    What happen when you delete `bashrc_linka` ?
    What happens when you delete `bashrc_linka` ?
    To understand the notion of **Inode** we need to know more about storage systems.
    ......@@ -230,11 +230,11 @@ You cannot dump data directly into the disk, you need to organize things to be a
    ![disk](./img/disk.png)
    Each media is divided into partition:
    Each media is divided into partitions:
    ![partitions](./img/partition.png)
    The media is divided into one or many partition, each of which have a file system type. Examples of file system type are:
    The media is divided into one or many partition, each of which have a file system type. Examples of file system types are
    - fat32, exFAT
    - ext3, ext4
    ......@@ -255,8 +255,8 @@ Find which disk is mounted at the root of the file tree.
    > We have seen the commands:
    >
    > - `stat` to display information on a file
    > - `less` to visualise the content of a file
    > - `ln` to create link
    > - `less` to visualize the content of a file
    > - `ln` to create links
    > - `mount` to list mount points
    [That’s all for the Unix file system, we will come back to it from time to time but for now you can head to the next section.](./5_users_and_rights.html)
    5_users_and_rights.Rmd
    + 9
    − 9
    View file @ d699debe
    ......@@ -63,7 +63,7 @@ Check your set of rights on your `.bashrc` file
    ls -l ~/.bashrc
    ```
    The first column of the `ls -l` output show the status of the rights on the file
    The first column of the `ls -l` output shows the status of the rights on the file
    ![user_rights](./img/user_right.png)
    ......@@ -121,7 +121,7 @@ What can you conclude on the symbols `+` , `=`, `-` and `,` with the `chmod` com
    > | `-r--r--r--` | 0444 | read |
    > | `-r-xr-xr-x` | 0555 | read & execute |
    > | `-rw-rw-rw-` | 0666 | read & write |
    > | `-rwxr-----` | 0740 | owner can read, write, & execute; group can only read; others have no permissions |
    > | `-rwxr-----` | 0740 | owner can read, write, & execute; group can only read; others have no permission |
    The default group of your user is the first in the list of the groups you belong to. You can use the command `groups` to display this list. What is your default group ?
    ......@@ -233,14 +233,14 @@ You can add a new user to your system with the command `useradd`
    useradd -m -s /bin/bash -g users -G adm,docker student
    ```
    - `-m` create a hone directory
    - `-m` create a home directory
    - `-s` specify the shell to use
    - `-g` the default group
    - `-G` the additional groups
    To log into another account you can use the command `su`
    What is the difference between the two following command ?
    What is the difference between the two following commands ?
    ```sh
    su student
    ......@@ -260,7 +260,7 @@ You can add new groups to your system with the command `groupadd`
    sudo groupadd dummy
    ```
    Then you can add users to these group with the command `usermod`
    Then you can add users to this group with the command `usermod`
    ```sh
    sudo usermod -a -G dummy student
    ......@@ -272,7 +272,7 @@ And check the result:
    groups student
    ```
    To remove an user from a group you can rewrite it's list of group with the command `usermod`
    To remove an user from a group you can rewrite its list of groups with the command `usermod`
    ```sh
    sudo usermod -G student student
    ......@@ -282,9 +282,9 @@ Check the results.
    # Security-Enhanced Linux
    While what you have seen in this section hold true for every Unix system, additionnal rules can be applied to control the rights in Linux. This is what is called [SE Linux](https://en.wikipedia.org/wiki/Security-Enhanced_Linux) (**s**ecurity-**e**nhanced **Linux**)
    While what you have seen in this section hold true for every Unix system, additional rules can be applied to control the rights in Linux. This is what is called [SE Linux](https://en.wikipedia.org/wiki/Security-Enhanced_Linux) (**s**ecurity-**e**nhanced **Linux**)
    When SE Linux is enabled on a system, every **processes** can be assigned a set of right. This is how, on Android for example, some programs can access your GPS while other cannot etc. In this case it's not the user rights that prevail, but the **process** launched by the user.
    When SE Linux is enabled on a system, every **process** can be assigned a set of rights. This is how, on Android for example, some programs can access your GPS while others cannot, etc. In this case it's not the user rights that prevail, but the **process** launched by the user.
    > We have seen the commands:
    >
    ......@@ -298,6 +298,6 @@ When SE Linux is enabled on a system, every **processes** can be assigned a set
    > - `sudo` to borrow **root** rights
    > - `groupadd` to create groups
    > - `groups` to list groups
    > - `usermod`to manipulate user's to groups
    > - `usermod`to manipulate users' groups
    [To understand more about processes you can head to the next section.](./6_unix_processes.html)
    0% or .
    You are about to add 0 people to the discussion. Proceed with caution.
    Finish editing this message first!
    Please register or to comment