From 6795135a2989c386ed0497d9db7723616c0a4286 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= <bneron@pasteur.fr>
Date: Fri, 2 Sep 2022 16:32:56 +0200
Subject: [PATCH] restructure course
split linux install in 2 chapters Install and admin
change Conda part in good practices which include cookiecutter and Conda
---
source/Conda/index.rst | 12 -
source/{Conda => Good_Practices}/conda.rst | 10 +-
source/Good_Practices/cookiecutter.rst | 14 ++
source/Good_Practices/index.rst | 13 +
source/Installation/factory_settings.rst | 2 +-
source/Installation/index.rst | 5 +-
source/Installation/linux_admin.rst | 230 ++++++++++++++++++
.../{linux.rst => linux_install.rst} | 9 +-
source/Installation/windows.rst | 8 +-
source/Unix/introduction.rst | 64 -----
source/Unix/module.rst | 85 -------
source/Unix/online_help.rst | 25 --
12 files changed, 278 insertions(+), 199 deletions(-)
delete mode 100644 source/Conda/index.rst
rename source/{Conda => Good_Practices}/conda.rst (97%)
create mode 100644 source/Good_Practices/cookiecutter.rst
create mode 100644 source/Good_Practices/index.rst
create mode 100644 source/Installation/linux_admin.rst
rename source/Installation/{linux.rst => linux_install.rst} (97%)
delete mode 100644 source/Unix/introduction.rst
delete mode 100644 source/Unix/module.rst
delete mode 100644 source/Unix/online_help.rst
diff --git a/source/Conda/index.rst b/source/Conda/index.rst
deleted file mode 100644
index 33e9f9d..0000000
--- a/source/Conda/index.rst
+++ /dev/null
@@ -1,12 +0,0 @@
-.. Conda for PHIND access training
-
-
-=====
-Conda
-=====
-
-
-.. toctree::
- :maxdepth: 2
-
- conda
diff --git a/source/Conda/conda.rst b/source/Good_Practices/conda.rst
similarity index 97%
rename from source/Conda/conda.rst
rename to source/Good_Practices/conda.rst
index 936106f..9593759 100644
--- a/source/Conda/conda.rst
+++ b/source/Good_Practices/conda.rst
@@ -281,6 +281,12 @@ Exercises
Extras
------
-* You find conda install too slow, try `mamba <https://mamba.readthedocs.io/en/latest/user_guide/mamba.html>`_. In your **base** environment::
+You find conda install
+* too slow,
+* consuming too memory
+* does not able to resolve dependencies either with anaconda or miniconda
+
+try `mamba <https://mamba.readthedocs.io/en/latest/user_guide/mamba.html>`_. In your **base** environment::
- conda install mamba
+ conda install mamba -n base -c conda-forge
+
diff --git a/source/Good_Practices/cookiecutter.rst b/source/Good_Practices/cookiecutter.rst
new file mode 100644
index 0000000..e5db8c3
--- /dev/null
+++ b/source/Good_Practices/cookiecutter.rst
@@ -0,0 +1,14 @@
+.. cookiecutter for Pasteur Network Course: Bioinformatics for SARS-CoV-2 sequence analysis
+
+
+.. _cookiecutter:
+
+======================
+Good project structure
+======================
+
+
+Cookiecutter
+============
+
+
diff --git a/source/Good_Practices/index.rst b/source/Good_Practices/index.rst
new file mode 100644
index 0000000..270c0bd
--- /dev/null
+++ b/source/Good_Practices/index.rst
@@ -0,0 +1,13 @@
+.. Good Practices for Pasteur Network Course: Bioinformatics for SARS-CoV-2 sequence analysis
+
+
+==============
+Good Practices
+==============
+
+
+.. toctree::
+ :maxdepth: 2
+
+ cookiecutter
+ conda
diff --git a/source/Installation/factory_settings.rst b/source/Installation/factory_settings.rst
index 1a503d6..88af50a 100644
--- a/source/Installation/factory_settings.rst
+++ b/source/Installation/factory_settings.rst
@@ -1,4 +1,4 @@
-.. Linux installation for PHIND access training
+.. Linux installation Pasteur Network Course: Bioinformatics for SARS-CoV-2 sequence analysis
.. _factory_settings:
diff --git a/source/Installation/index.rst b/source/Installation/index.rst
index e00c0fc..163cde9 100644
--- a/source/Installation/index.rst
+++ b/source/Installation/index.rst
@@ -1,4 +1,4 @@
-.. Linux installation for PHIND access training
+.. Linux Pasteur Network Course: Bioinformatics for SARS-CoV-2 sequence analysis
==================
Linux Installation
@@ -9,5 +9,6 @@ Linux Installation
factory_settings
windows
- linux
+ linux_install
+ linux_admin
diff --git a/source/Installation/linux_admin.rst b/source/Installation/linux_admin.rst
new file mode 100644
index 0000000..504d1df
--- /dev/null
+++ b/source/Installation/linux_admin.rst
@@ -0,0 +1,230 @@
+.. Linux administration for Pasteur Network Course: Bioinformatics for SARS-CoV-2 sequence analysis
+
+.. _linux_admin:
+
+====================
+Linux administration
+====================
+
+
+Introduction
+============
+
+
+What is Unix?
+-------------
+
+* Unix, Linux, \*\ nix, …. : What is it?
+* Operating System
+* Created in 1969 in the Bell Labs
+* Multi-user
+* Multi-task
+* Protected memory
+* Unix family: BSD, Linux, Mac OS X (Darwin), Android, etc.
+
+
+Why use Unix on the computing servers?
+--------------------------------------
+
+* Fares well in the scientific domain
+* Multi-user
+* Versatile
+* Powerful
+
+
+What is the Unix shell?
+-----------------------
+
+* a shell is a user interface for access to an **operating system**'s services.
+* a shell can be a **command line interface** or a **graphical user interface**
+* in a command line interface, the user issues commands to the program in the form of successive lines of text (command lines).
+* what is commonly referred as "Unix shell" is a set of commonly-used CLI programs.
+
+
+Commands
+--------
+
+* A command is an instruction you send to the shell to ask it to execute an action.
+
+
+Syntax: command, options, arguments
+"""""""""""""""""""""""""""""""""""
+
+* the command: what action should be executed
+* the arguments: the object of the action
+* the options: flags that specify or modify the behaviour of the command
+
+ * options are usually preceded by
+
+ * ``-`` if its a one letter option
+ * ``--`` if its a word option
+
+ ::
+
+ command <options> <aguments>
+
+ ls -a
+ ls --all
+
+
+
+On line Help
+------------
+
+get help
+""""""""
+
+* **man command or program** displays the on-line manual pages.
+* **info command or program** Read documentation.
+* **help command or program** help retrieve information about bash commands only.
+
+
+man vs info vs help
+"""""""""""""""""""
+* **man** pages are the UNIX traditional way of distributing documentation about programs.
+* In the early '90s, the GNU project decided that "man" documentation system was outdated, and wrote the **info** command to replace it.
+* **help** is a bash command. It uses internal bash structures to store and retrieve information about bash commands.
+
+
+
+set the date and time
+=====================
+
+
+
+sudoers
+=======
+
+In most of distros, there is a special user named `root` which have the rights to do anything.
+This role is dangerous so to avoid mistake we reserved to special action and take care at what we do
+when we are logged as root.
+
+Debian/Ubuntu have no root user anymore, but some user are granted for some special operations that need root privileges.
+The first user you created during the installation phase is sudoer. and is granted for all root privilege for all operation.
+to be granted and execute a command with the root privilege, you need to precede your command by the keyword sudo (super user do)
+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::
+
+ sudo useradd ...
+
+
+create new user
+===============
+
+.. code-block:: shell
+
+ sudo useradd -u UID -g <primary group> -G <group1,group2,...> -m --shell /bin/bash
+
+only root can perform this command
+
+create new group
+================
+
+.. code-block:: shell
+
+ sudo groupadd <name of group>
+
+only root can perform this command
+
+To take in account new user and group you need to logout and login again
+
+check you identity
+==================
+
+whoami
+------
+
+id
+--
+
+access to external hard drive
+=============================
+
+
+
+install package
+===============
+
+Linux distinguish from other operating system by packaging lot of software.
+and a package management system.
+Each linux distros have it's own packaging system:
+
+* centos/redhat have yum/dnf package management system and .rpm packages
+* debian/ubuntu have apt package management system with .deb packages
+* gentoo have portage package management system with .ebuild packages
+
+
+The advantages of official packages is that the installation of these software is easy and well tested.
+The maintenance of these package is ensure by the packages manager.
+Lot of bioinformatics software are packages in these distros.
+
+The inconvenient of these packages is that often the latest bleeding edge version of software is not available.
+The package manager can handle only one version of each package at one time
+(for instance you cannot use blast+2.11 for one project and 2.0 for an other one).
+the packages are upgrade when you upgrade the system, so the version can change during a project life time.
+We will see alternatives
+
+
+search
+------
+
+To search if a software is packaged for your ubuntu use the apt command
+
+.. code-block::
+
+ apt search <soft name>
+
+the low level command, to use if it's inside a script (dockerfile, ...)
+
+.. code-block::
+
+ apt-cache search <soft name>
+
+
+install
+-------
+
+To install a package, once you have the exact name of the package you want to install
+
+.. code-block::
+
+ sudo apt install <package name>
+
+.. code-block::
+
+ sudo apt-get install <package name>
+
+
+ .. note::
+
+ notice that anybody can search if a package exists, but only users granted can install a new package.
+
+
+Update system
+=============
+
+To update the whole system (all packages), it can be perform via a widget "software updater",
+but I will describe below the command line way.
+
+You need to update the list of package, then perform the upgrade of the packages
+
+.. code-block::
+
+ sudo apt update
+ sudo apt upgrade
+
+.. code-block::
+
+ sudo apt-get update
+ sudo apt-get upgrade
+
+Debian/Ubuntu is a distros based on release, sometimes you need to switch to a new release.
+For that you need to perform a `distupgrade` but only when a new release is available.
+You will warn of new release by the package manager after a "classical" update operation.
+
+.. code-block::
+
+ sudo apt-get distupgrade
+
diff --git a/source/Installation/linux.rst b/source/Installation/linux_install.rst
similarity index 97%
rename from source/Installation/linux.rst
rename to source/Installation/linux_install.rst
index e7fcc41..ab083df 100644
--- a/source/Installation/linux.rst
+++ b/source/Installation/linux_install.rst
@@ -1,4 +1,4 @@
-.. Linux installation for PHIND access training
+.. Linux installation for Pasteur Network Course: Bioinformatics for SARS-CoV-2 sequence analysis
.. _linux:
@@ -89,13 +89,13 @@ Select the keyboard layout
Choose the installation mode
-"""""""""""""""""""""""""""
+""""""""""""""""""""""""""""
we will use
* normal installation mode
* with download the update (available only if yoy are connected to internet)
* and third party drivers installation (available only if yoy are connected to internet)
-.. image:: ../_static/install/linux_install_mode.jpg
+.. image:: ../_static/install/linux_select_install_mode.jpg
Dual boot
@@ -180,9 +180,10 @@ check you identity
==================
whoami
+------
id
-
+--
install package
===============
diff --git a/source/Installation/windows.rst b/source/Installation/windows.rst
index ba0790f..cdb6929 100644
--- a/source/Installation/windows.rst
+++ b/source/Installation/windows.rst
@@ -1,4 +1,4 @@
-.. Linux installation for PHIND access training
+.. Linux installation for Pasteur Network Course: Bioinformatics for SARS-CoV-2 sequence analysis
.. _windows:
@@ -11,13 +11,13 @@ boot on windows 10 key
put the computer on and press `escape` to enter in boot menu
-.. image:: ../_static/install/windows_boo_key.jpg
+.. image:: ../_static/install/windows_boot_key.jpg
select windows lang
===================
-.. image:: ../_static/install/select_lang.jpg
+.. image:: ../_static/install/linux_select_lang.jpg
install windows
@@ -47,7 +47,7 @@ rearange partition table
so we now have 476.5Go not allocated partition, taht we split in two
-.. image:: ../_static/install/windows_new_partiion.jpg
+.. image:: ../_static/install/windows_new_partition.jpg
select the not allocated space, click on `new` then ste the size 204800 Mo (200 Go * 1024)
diff --git a/source/Unix/introduction.rst b/source/Unix/introduction.rst
deleted file mode 100644
index 3ce9245..0000000
--- a/source/Unix/introduction.rst
+++ /dev/null
@@ -1,64 +0,0 @@
-.. _Introduction:
-
-************
-Introduction
-************
-
-
-What is Unix?
-*************
-
-* Unix, Linux, *\ nix, …. : What is it?
-* Operating System
-* Created in 1969 in the Bell Labs
-* Multi-user
-* Multi-task
-* Protected memory
-* Unix family: BSD, Linux, Mac OS X (Darwin), Android, etc.
-
-
-Why use Unix on the computing servers of the Institut Pasteur?
-**************************************************************
-
-* Fares well in the scientific domain
-* Multi-user
-* Versatile
-* Powerful
-
-
-What is the Unix shell?
-***********************
-
-.. rst-class:: build
-
- * a shell is a user interface for access to an **operating system**'s services.
- * a shell can be a **command line interface** or a **graphical user interface**
- * in a command line interface, the user issues commands to the program in the form of successive lines of text (command lines).
- * what is commonly referred as "Unix shell" is a set of commonly-used CLI programs.
-
-
-Commands
-********
-
-* A command is an instruction you send to the shell to ask it to execute an action.
-
-
-Syntax: command, options, arguments
-===================================
-
-* the command: what action should be executed
-* the arguments: the object of the action
-* the options: flags that specify or modify the behaviour of the command
-
- * options are usually preceded by
-
- * ``-`` if its a one letter option
- * ``--`` if its a word option
-
- ::
-
- command <options> <aguments>
-
- ls -a
- ls --all
-
diff --git a/source/Unix/module.rst b/source/Unix/module.rst
deleted file mode 100644
index ad0a661..0000000
--- a/source/Unix/module.rst
+++ /dev/null
@@ -1,85 +0,0 @@
-.. _Module:
-
-
-******
-Module
-******
-
-
-why module
-==========
-
-* The softwares evolve very quickly in bioinformatics.
-* The new versions give not always the same results.
-* We need to have several versions installed at the same time.
-
-what is module
-==============
-
-* *module* allow to load dynamically a package with a specified version on demand.
-* *module* modify the environment dynamically.
-
-
-what is available
-=================
-
-To know what package are available:
-
-* ``module av`` display all available packages.
-* ``module av bla`` display all available packages **begining** by *bla*
-
-
-do a program available
-======================
-
-* ``module load package/vers`` load the package.
-* ``module list`` list all packages loaded in the environment.
-* ``module unload package/vers`` unload a package.
-* ``module purge`` unload all loaded packages.
-
-get help on a module
-====================
-
-* ``module help package/vers`` display help about the package.
-
-your own modulefiles
-====================
-
-Why write your own modulefiles
-
-* ``share controled environment`` among your workmates
-* ``share coherent programs and alias`` among your workmates
-* ``set up specific tools and pipelines`` with control
-
-* see ``man modulefile`` for the syntax to use.
-
-use your own private modulefiles
-================================
-
-* place your modulefiles under ``~/privatemodules``
-* ``module load use.own`` your modulefiles wil be available for all module commands
-
-
-use shared private modulefiles
-================================
-
-* place the modulefile under a directory with ``read permissions`` for all users you want to share.
-* tell users to isue the command ``module use`` the given directory, they will gain acces to your modulefiles.
-
-where is hide my program?
-=========================
-
-
-* ``whatprovides program`` list all package that provides the program.
-
-exercises
-
-* what modules provides blastp?
-* load the right module.
-
-
-
-module documentation
-====================
-
-* https://projets.pasteur.fr/projects/modules/wiki
diff --git a/source/Unix/online_help.rst b/source/Unix/online_help.rst
deleted file mode 100644
index 339e770..0000000
--- a/source/Unix/online_help.rst
+++ /dev/null
@@ -1,25 +0,0 @@
-.. _Online_Help:
-
-************
-On line Help
-************
-
-
-get help
-========
-
-* **man command or program** displays the on-line manual pages.
-* **info command or program** Read documentation.
-* **help command or program** help retrieve information about bash commands only.
-
-
-man vs info vs help
-===================
-
-* **man** pages are the UNIX traditional way of distributing documentation about programs.
-* In the early '90s, the GNU project decided that "man" documentation system was outdated, and wrote the **info** command to replace it.
-* **help** is a bash command. It uses internal bash structures to store and retrieve information about bash commands.
-
-exercises
-=========
-
\ No newline at end of file
--
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