add section about apptainer exec/shell command

source/Good_Practices/containers.rst

@@ -322,6 +322,20 @@ So the complete command line will be:
     docker run -v $PWD:/home/msf  -u $(id -u ${USER}):$(id -g ${USER}) gempasteur/macsyfinder:2.0 macsyfinder --sequence-db /home/msf/genome.fasta ...
 
 
+You can also enter and work interactively in the container
+
+you have to add options
+
+* `-i` for *interactive*
+* `-t` to allocates a pseudo tty
+* and depending how the image is build override  the entrypoint --entrypoint
+
+.. code-block::
+
+    docker run -v $PWD:/home/msf  -u $(id -u ${USER}):$(id -g ${USER}) -it --entrypoint /bin/bash gempasteur/macsyfinder:2.0
+
+:code:`CTRL d` to exit of the container
+
 
 Exercise
 """"""""
@@ -502,6 +516,86 @@ For the other guys (mac, windows, ...)
 You have to install from the sources see  https://apptainer.org/docs/user/main/quick_start.html#quick-start
 
 
+Build macsyfinder Apptainer image from Docker image
+'''''''''''''''''''''''''''''''''''''''''''''''''''
+
+If there is a Docker image available on docker hub it is very easy to convert it into  Apptainer image.
+
+:code:`apptainer build <image_name> docker://<docker_image:tag>`
+
+:code:`apptainer build macsyfinder.img docker://gempasteur/macsyfinder:2.0`
+
+It will create a file `macsyfinder.img`. The Apptainer images are regular files.
+You can manipulates as files mv/copy/transfert to a collaborator, ...
+
+.. note::
+
+    build from docker is the only build way to build an image without to be root/sudoer
+
+
+Run macsyfinder on real data
+''''''''''''''''''''''''''''
+
+:code:`apptainer run <image_name> <argument and options specific to the image>`
+
+.. code-block::
+
+    apptainer run macsyfinder.img macsyfinder --sequence-db /home/msf/genome.fasta ...
+
+If your data is in your HOME they are accessible inside the container with the same path.
+If your data are elsewhere on the file system, you have to bind them explicitly
+
+For instance if my data are */pasteur/projects/msf_analysis/data* I can bind /pasteur in the container
+with the option `-B/ --bind <src on host>:<dest in container>` if *src* and *dest* are the same, dest can be omitted.
+
+
+.. code-block::
+
+    apptainer run -B /pasteur macsyfinder.img macsyfinder --sequence-db /home/msf/genome.fasta ...
+
+I bind */pasteur* on the host to */pasteur* inside the container. So the path will be identical on host and in container.
+
+.. note::
+
+    It's not a problem to bind /pasteur even there are lot of project belonging to other teams.
+    I as run container under my id I have the same rights as on hosts. So if I cannot access to /pasteur/projects/whatever
+    on the host, I can bind it in container but I cannot access to it (read/write/...).
+
+.. note::
+
+    You can run directly from docker image, apptainer will download it and convert it on the fly.
+    The resulting image is located in apptainer cache
+
+    :code:`apptainer run -B /pasteur docker:gempasteur/macsyfinder macsyfinder --sequence-db /home/msf/genome.fasta ...`
+
+
+You can execute any arbitrary command line in a context of an Apptainer container
+
+.. code-block::
+
+    apptainer exec -B /pasteur macsyfinder.img ls -l /pasteur
+
+
+You can also enter interactively in the container
+
+.. code-block::
+
+    apptainer shell -B /pasteur macsyfinder.img
+
+.. warning::
+
+    By default the container is not writable.
+
+To be allowed to write something in your interactive session
+
+* you must run the command as `sudo`
+* adn add the `-w/--writable` option
+
+.. code-block::
+
+    sudo apptainer shell --writable macsyfinder.img
+
+
 
 Exercise
 """"""""