Create modules.md

modules.md

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+
+> 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