From b17cb0ad31a5e5efac1b9a8e1a3c71854d082fce Mon Sep 17 00:00:00 2001
From: Eve Zeyl Fiskebeck <45561997+evezeyl@users.noreply.github.com>
Date: Mon, 16 Sep 2019 13:38:33 +0200
Subject: [PATCH 1/3] Create modules.md

---
 modules.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 modules.md

diff --git a/modules.md b/modules.md
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/modules.md
@@ -0,0 +1 @@
+

From 4e27fbbf905bbdbe46b8d36c1c84b4e98393fe6c Mon Sep 17 00:00:00 2001
From: Eve Zeyl Fiskebeck <45561997+evezeyl@users.noreply.github.com>
Date: Mon, 16 Sep 2019 13:53:47 +0200
Subject: [PATCH 2/3] Update modules.md

---
 modules.md | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/modules.md b/modules.md
index 8b13789..5af9f10 100644
--- a/modules.md
+++ b/modules.md
@@ -1 +1,54 @@
 
+> put in clear notes from Thomas presentation 16/09/2019 On making our own modules
+
+You can create modules in your own work folder on Abel: $HOME equivalent to `/usit/abel/u1/username`
+
+NB: to see the path represented by the $HOME variable do `echo $HOME`
+
+example:
+```
+cd $HOME
+git clone https://github.com/lh3/seqtk.git
+cd seqtk
+make
+./seqk # to launch from the directory
+```
+To be able to load those modules you have to options
+
+1) Add the path where the software is to your login script `.bash_login`
+
+$PATH:...
+
+2) create a module for this software and load the module when the software is needed
+
+# Create and use your own modules on Abel 
+
+1) create a directory `modules` on your own area: $HOME
+```
+cd modules
+ls
+```
+All the files listed are text files describing of where the computing ressource will find the the softwares that are installed in modules
+
+A "module file" contains details about applications, description of what the module is, commands that will be launched when you load this module file: in other words: everything that will be loaded and added to the $PATH
+> What is the $PATH ? its where the computer looks for softwares to exectute ...documents? 
+
+Eve: NB: see in the HTP advancesd course -> now remember was things about modules
+
+2) in your .bash_login:
+
+Export path of softwares and modules we can use. 
+
+
+Module environment 
+
+3) Launching module - identical as Abel own modules
+
+`module launch module_name/version`
+
+> version if you want to use a version different than the default version
+
+# Links
+[environment modules documentation](https://modules.readthedocs.io/en/latest/index.html)
+
+> for those with experimental ideas ... can do on ubuntu PC -> will use that to test first

From cefc5938325242c50262c7fbaf5ac14ed3d39659 Mon Sep 17 00:00:00 2001
From: Eve Zeyl Fiskebeck <45561997+evezeyl@users.noreply.github.com>
Date: Mon, 16 Sep 2019 14:14:22 +0200
Subject: [PATCH 3/3] deleted - was wrong file name

---
 own_modules.md | 2 --
 1 file changed, 2 deletions(-)
 delete mode 100644 own_modules.md

diff --git a/own_modules.md b/own_modules.md
deleted file mode 100644
index 0bbd02c..0000000
--- a/own_modules.md
+++ /dev/null
@@ -1,2 +0,0 @@
-Own modules install - Thomas
-