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title: IFB (Institu Français de bio-informatique) Cloud
author: "Laurent Modolo"
output:
rmdformats::downcute:
self_contain: false
use_bookdown: true
default_style: "light"
lightbox: true
css: "./www/style_Rmd.css"
```{r include = FALSE}
if (!require("fontawesome")) {
install.packages("fontawesome")
}
if (!require("klippy")) {
install.packages("remotes")
remotes::install_github("rlesur/klippy")
}
library(fontawesome)
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(comment = NA)
klippy::klippy(
position = c('top', 'right'),
color = "white",
tooltip_message = 'Click to copy',
tooltip_success = 'Copied !')
```
<a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">
<img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" />
</a>
## IFB (Institu Français de bio-informatique) Cloud
[](http://creativecommons.org/licenses/by-sa/4.0/)
Objective: Start and connect to an appliance on the IFB cloud
Instead of working on your computer where you don't have an Unix-like OS or have limited right, we are going to use the [IFB (Institu Français de bio-informatique) Cloud]( https://biosphere.france-bioinformatique.fr/).
1. Access the [**https://biosphere.france-bioinformatique.fr/**](https://biosphere.france-bioinformatique.fr/) website
Instead of working on your computer where you don't have an Unix-like OS or have limited right, we are going to use the [IFB (Institu Français de bio-informatique) Cloud]( https://biosphere.france-bioinformatique.fr/). For this you will need:
1. Access the [**https://biosphere.france-bioinformatique.fr/**](https://biosphere.france-bioinformatique.fr/) website
2. On the top right of the screen click on <img src="./img/signin_ifb.png" alt="sign in" style="zoom:150%;" />
3. Then click on 
4. Use the **Incremental search field** to select your identity provider (CNRS / ENS de Lyon / etc.)
5. Login
6. Complete the form with your **Name**, **First Name**, **Town** and **Zip Code**. You can ignore the other field and click on **accept**.
7. Go to your **Groups** parameters on the top right 
8. Click on  and type **LBMC Unix 2020**
9. You can click on the **+** sign to register and wait to be accepted in the group
### Starting the LBMC Unix 2020 appliance
To follow this practical you will need to start the **[LBMC Unix 2020](https://biosphere.france-bioinformatique.fr/catalogue/appliance/177/)** appliance from the [IFB Cloud](https://biosphere.france-bioinformatique.fr/) and click on the  button after login with your account.
In the IFB jargon, appliance means **virtual machine** (VM). Remember how a universal Turing machine can run any programs ? A virtual machine, is a simulation program, simulating a physical computer. VM's have the following advantages:
- Copies of the VM will be identical (there will be no differences between your running *LBMC Unix 2020 appliance* and mine )
- Upon starting the VM is reset to the *LBMC Unix 2020 appliance* state
- You can break everything in your VM, terminate it and start a new one.
To access to your appliance you can go to the [**myVM** tab](https://biosphere.france-bioinformatique.fr/cloud/)
You will see the list of your running or starting appliances.
**Don't forget to terminate your appliances at the end of the session by clicking on** 
You will need to start this appliance at the start of each session of this course and terminate it afterward.
The  symbol indicates that your appliance is starting.
### Accessing the LBMC Unix 2020
You can open the **https** link next to the termination button of your appliance in a new tab. You will have the following message
This means that the https connection is encrypted with a certificate unknown to your browser. As this certificate is going to be destroyed when you terminate your appliance, we don't want to pay a certification authority to validate it. Therefore you can safely add an exception for this certificate.
The webpage you will load will display only the following line:
```sh
achinea3e18205-1f8c-4ee1-995e-d33ef57afa3c login:
```
To get your identification information you can click on the **Params** next to the **https** link.
**The password and the https links are one of the only things that going to change when you start a new appliance.**
```sh
Password:
```
To copy / paste your password, you will need to perform a right-click and select **past from the browser.**

Then paste your password in the dialog box.
Don't worry the password will not be displayed (not even in the form of `*****`, so someone looking at your screen will not be able to guess it's length), you can press **enter** to log on your VM.
[First steps in a terminal.](./3_first_steps_in_a_terminal.html)