add content about disk usage and space left

source/Installation/linux_admin.rst

 .. Linux administration for Pasteur Network Course: Bioinformatics for SARS-CoV-2 sequence analysis
 
+.. role:: red
+
 .. _linux_admin:
 
 ====================
@@ -115,10 +117,25 @@ to be granted and execute a command with the root privilege, you need to precede
 The first time you execute a command as sudo you will ask to confirm your password.
 Your password is available for one shell, so if you execute a second command in an other terminal you will ask again for your password.
 
-.. code-block::
+.. code-block:: shell
 
     sudo useradd ...
 
+allow one user to be sudoers just add it in group ``sudo``
+
+.. code-block:: shell
+
+    sudo usermod -a -G sudo <username>
+
+This command a <username> in the secondary group ``sudo``
+
+To fine tune the sudoers permission you have to edit the sudoers configuration file
+withe the command
+
+.. code-block:: shell
+
+    sudo visudo
+
 
 create new user
 ===============
@@ -147,16 +164,166 @@ check you identity
 whoami
 ------
 
+To know your login
+
 id
 --
 
+to know your
+
+* login/uid
+* primary group/gid
+* all secondaries groups user belong to
+
+.. code-block:: shell
+
+    $ id
+    uid=1000(cronos) gid=10010(cronos) groups=1001(cronos),4(adm),24(cdrom),27(sudo),48(docker),100(users), ...
+    $ id cronos
+    uid=1000(cronos) gid=10010(cronos) groups=1001(cronos),4(adm),24(cdrom),27(sudo),48(docker),100(users), ...
+
+
 access to external hard drive
 =============================
 
+All files accessible in a Unix system are arranged in one big tree, the file hierarchy, rooted at /.
+These files can be spread out over several devices.
 
+.. note::
 
-install package
-===============
+    A quick note on the filesystem: it’s a hierarchy of directories that systems use to organize file(s) and folder(s) on a storage media.
+    Filesystem exists in every single storage solution:
+    USB flash drive, CD-ROM, HDD, SSD, and even floppy disks! In the case of UNIX/Linux and similar systems,
+    the filesystem starts with the root directory (noted as “/”).
+    Under “root”, all the other child filesystems exist.
+
+The mount command serves to attach the file system found on some device to the big file tree.
+
+basics
+
+
+When you insert usbkey in your computer, xubuntu detect it and trigger a mount command
+
+Unfortunately it does not do the same for filesystem on network.
+it will be case to connect the PC to the mk1c sequencer.
+So we will have to mount manually the filesystem of the sequencer on our machine to use allow ``rampart`` to access
+to the data in realtime.
+
+We saw that mount include a device on the our local file system
+So we need to know
+
+- which device
+- a location where to mount the device we called mounting point
+  The mounting point is just a regular directory.
+- there are several filesystem formats ext4,vfat, .... so we need to specify which protocol
+- only root can mount a new device
+
+
+    sudo mount -t <format> <device> <mounting point> <option>
+
+In our case the mk1c export its filesystem over network with the cifs protocol
+
+To do only Once
+
+    sudo mkdir -p /mnt/mk1c
+
+To do each time you need to connect the Pc to the mk1c
+
+    sudo mount -t cifs //mk1c ip address/data  -ousername=<the user on mk1c>,uid=<your uid on the Pc>,gid=<your primary gid on the Pc> /mnt/mk1c
+
+    $ sudo mount -t cifs //192.168.0.10/data -ousername=minit,uid=1000,gid=1000 /mnt/mk1c
+    passowrd ******
+
+    ls -l /mnt/mk1c
+
+
+Conversely, the umount command will detach it again.
+
+    to deconnect the Pc from the mk1c
+
+    sudo umount /mnt/mk1c
+
+
+The storage system is not infinite
+==================================
+
+Any hard drive have a size.
+Sequencing generate data.
+You have to monitor the size used and free on the mk1c, otherwise you risk to have an error
+``No space left on device`` and you :red:`will lost the run`.
+
+df
+--
+The `df` command stands for “disk filesystem“,
+it is used to get a full summary of available and used disk space usage of the file system on the Linux system.
+
+`df` without option or argument display space usage for all mounted devices
+
+.. code-block::
+
+    $ df
+    Filesystem     1K-blocks     Used Available Use% Mounted on
+    tmpfs            1559800     2016   1557784   1% /run
+    /dev/nvme0n1p5 284239328 20531532 249196232   8% /
+    tmpfs            7798984        0   7798984   0% /dev/shm
+    tmpfs               5120        4      5116   1% /run/lock
+    /dev/nvme0n1p1    262144    33432    228712  13% /boot/efi
+    tmpfs            1559796       92   1559704   1% /run/user/1000
+
+
+The `-h` *stand for humam readable* dispaly the same information but the size is converted in Ko/Mo/Go
+
+.. code-block::
+
+    $ df -h
+    Filesystem      Size  Used Avail Use% Mounted on
+    tmpfs           1.5G  2.1M  1.5G   1% /run
+    /dev/nvme0n1p5  272G   20G  238G   8% /
+    tmpfs           7.5G     0  7.5G   0% /dev/shm
+    tmpfs           5.0M  4.0K  5.0M   1% /run/lock
+    /dev/nvme0n1p1  256M   33M  224M  13% /boot/efi
+    tmpfs           1.5G   92K  1.5G   1% /run/user/1000
+
+You ca restraint the display to one device here / is for the root filesystem
+
+.. code-block::
+
+    $ df -h /
+    Filesystem      Size  Used Avail Use% Mounted on
+    /dev/nvme0n1p5  272G   20G  238G   8% /
+
+du
+--
+
+Conversely `du` show you the space used by some files / directories
+
+one very useful command with du is with options
+
+* -h for human readable
+* -s summary instead to show you the size of all files and recursively files in directories,
+  it display only the size of the level ask and display the size used by the directory (not each files inside directories
+
+.. code-block::
+
+    $ cd
+    $ du -sh *
+    30M     artic-ncov2019
+    30M     Desktop
+    4.0K    Documents
+    508K    Downloads
+    5.3G    miniconda3
+    59M	    Miniconda3-py39_4.9.2-Linux-x86_64.sh
+    4.0K    Music
+    4.0K    Pictures
+    4.0K    Public
+    350M    snap
+    20K     Templates
+    4.0K    Videos
+
+
+
+Installing package
+==================
 
 Linux distinguish from other operating system by packaging lot of software.
 and a package management system.
@@ -237,5 +404,5 @@ You will warn of new release by the package manager after a "classical" update o
 
 .. code-block::
 
-    sudo apt-get distupgrade
+    sudo apt dist-upgrade