From e472931b88d418a3f0682e06165e9601a91365b7 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Thu, 7 Mar 2024 12:31:36 +0100
Subject: [PATCH] externalize setup folder structure
---
docs/pages/bash/bash-0-setup.md | 19 ++++++++++++
docs/pages/bash/bash-2-the-basics.md | 4 +++
docs/pages/bash/bash-3-navigating.md | 29 ++++++-------------
...sh-4-working_with_files_and_directories.md | 11 +++++--
4 files changed, 41 insertions(+), 22 deletions(-)
create mode 100644 docs/pages/bash/bash-0-setup.md
diff --git a/docs/pages/bash/bash-0-setup.md b/docs/pages/bash/bash-0-setup.md
new file mode 100644
index 0000000..76a1215
--- /dev/null
+++ b/docs/pages/bash/bash-0-setup.md
@@ -0,0 +1,19 @@
+### Setup
+
+
+First copy and paste this command to execute it. No worries not need to understand what it does.
+
+```bash
+course={{extra.working_directory}}
+mkdir -p ~/$course/script
+mkdir -p ~/$course/data
+echo "Welcome to the {{extra.working_directory}} course" > ~/$course/README
+echo "echo hello" > ~/$course/script/script1.sh
+echo "ATGC" > ~/$course/data/data1.fa
+touch ~/$course/data/dataA.fastq
+touch ~/$course/data/dataB.fastq
+cd $course
+echo "done"
+```
+
+The command above prepare a {{extra.working_directory}} directory with material.
diff --git a/docs/pages/bash/bash-2-the-basics.md b/docs/pages/bash/bash-2-the-basics.md
index 65386d0..c487975 100644
--- a/docs/pages/bash/bash-2-the-basics.md
+++ b/docs/pages/bash/bash-2-the-basics.md
@@ -71,6 +71,10 @@ Bash is often preferred over other shells for many reasons:
## The Unix directory structure
+{%
+ include-markdown "pages/bash/bash-0-setup.md"
+%}
+
**/ – The root directory**
Everything, all the files and directories, in Linux are located under `root` represented by `/`. If you look at the directory structure, you’ll realize that it is similar to a plant’s root.
diff --git a/docs/pages/bash/bash-3-navigating.md b/docs/pages/bash/bash-3-navigating.md
index 1429494..c0097fb 100644
--- a/docs/pages/bash/bash-3-navigating.md
+++ b/docs/pages/bash/bash-3-navigating.md
@@ -2,25 +2,11 @@
Back to the directory structure... this time we will learn to `navigate between directories` and the difference between **absolute** and **relative** paths.
-## Prepare
+??? quote "First click and follow the instructions below only if you start the course at this stage! Otherwise skip this step!"
+ {%
+ include-markdown "pages/bash/bash-0-setup.md"
+ %}
-Back to the directory structure... this time we will learn difference between **absolute** and **relative** path and use a few commands in process.
-
-First copy and paste this command to execute it. No worries not need to understand what it does.
-
-```bash
-course={{extra.working_directory}}
-mkdir -p ~/$course/script
-mkdir -p ~/$course/data
-echo "Welcome to the {{extra.working_directory}} course" > ~/$course/README
-echo "echo hello" > ~/$course/script/script1.sh
-echo "ATGC" > ~/$course/data/data1.fa
-touch ~/$course/data/dataA.fastq
-touch ~/$course/data/dataB.fastq
-echo "done"
-```
-
-The command above prepare a {{extra.working_directory}} directory with material.
## Where are we?
@@ -121,7 +107,7 @@ To move into a directory we have seen we can use the command `cd` and a director
## Relative path
-A `relative`` path is a path that specifies the location of a file or directory with respect to the current working directory. Any path that does not begin with a separator character ("/") is a relative path.
+A `relative` path is a path that specifies the location of a file or directory with respect to the current working directory. Any path that does not begin with a separator character ("/") is a relative path.
!!! tip
Relative path:
@@ -190,12 +176,15 @@ We are now in the `script` directory.
1. cd .
2. cd ..
3. cd ../..
- 4. cd /home/<userName>
+ 4. cd /home/<userName\>
5. cd ~
6. cd home
7. cd ~/data/..
9. cd /
+??? example "Click to show the solution"
+ 3,4,5
+
## File path Autocompletion
It exist a wonderful behavior in Bash called the autocompletion. What it is?
diff --git a/docs/pages/bash/bash-4-working_with_files_and_directories.md b/docs/pages/bash/bash-4-working_with_files_and_directories.md
index 4f63def..f987b48 100644
--- a/docs/pages/bash/bash-4-working_with_files_and_directories.md
+++ b/docs/pages/bash/bash-4-working_with_files_and_directories.md
@@ -1,7 +1,14 @@
# Working with files and directories
-In theory you should be in the `script` directory.
-Check using `pwd` and if it is not the case run `cd ~/{{extra.working_directory}}/script`
+??? quote "First click and follow the instructions below only if you start the course at this stage! Otherwise skip this step!"
+ {%
+ include-markdown "pages/bash/bash-0-setup.md"
+ %}
+
+Let's be sure to be in the `script` directory before to continue the rest of the training:
+```bash
+cd ~/{{extra.working_directory}}/script
+```
{: style="height:250px"}
--
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