Galaxy Initiation

name: inverse
layout: true
class: center, middle, inverse

---
layout: false
background-image: url("../images/presentation.png")
<div style="position: absolute; bottom: 0%; left: 1%; color: white" >
<h3 style="position: relative; width:400px; height:70px">Upload Data in Galaxy@Pasteur</h3>
<h4>Olivia Doppelt-Azeroual, Fabien Mareuil</h4>
</div>
<img style="position: absolute; top: 2%; right: 2%" src="../images/LogoIP-CNRS-C3BI-NBV4small-e1460524231316.png" width="200">

---
## Upload a data if size is **>** 2Go (command line) (1/2)

*Command line (Terminal) solution*
* To establish the connection with the sftp server from your Linux or Mac computer:  
```bash
sftp -P 2222 yourlogin@galaxy.pasteur.fr
```
or
```bash
sftp -oPort=2222 yourlogin@galaxy.pasteur.fr
```
* Remark if data are on tars, first connect to it (with your pasteurID password):  
```bash
ssh yourlogin@tars.pasteur.fr
```
.center[**REMARK: Use the galaxy password for the sftp connection**]
---
## Upload a data if size is **>** 2Go  (command line) (2/2)

*Command line (Terminal) solution*
* To upload a file on the sftp server:
```bash
sftp>put PathToYourFile
```
* To upload a directory on the sftp server:
    * On the sftp server create a directory with the same name that the directory you wish to upload:
    ```bash
    sftp>mkdir mydirectory
    sftp>put -r mydirectory
    ```

---
## Upload a data if size is **>** 2Go (Filezilla)

*Filezilla solution*: You can use filezilla to transfer data from your computer to your Galaxy transfer directory 
* Launch filezilla
* Open the site manage: ctrl+s 
* Click on new site
   * host: galaxy.pasteur.fr
   * port: 2222
   * Protocol: sftp - ssh File Transfer Protocol
   * Logon Type: Ask for password **galaxy password**
   * User: yourlogin
* Drag'n drop your data from the left windows to the right windows
<img src="../images/filezilla.png" width="100%" height="100%" align="center" valign="center">

---
## Upload a data if size is **>** 2Go (in Galaxy) (1/2)

* Then use the galaxy web interface to transfer the data in your Galaxy library 
* Click on your library
<img src="../images/shared_data_1.png" width="100%" height="100%" align="center" valign="center">
* It's possible to create folder to organize your data
<img src="../images/shared_data_2.png" width="100%" height="100%" align="center" valign="center">
* To upload file you transfered in your link directory (from User Directory):
<img src="../images/shared_data_3.png" width="100%" height="100%" align="center" valign="center">

---
## Upload a data if size is **>** 2Go (in Galaxy) (2/2)

<img src="../images/shared_data_4.png" width="100%" height="100%" align="center" valign="center">
* Then select your data and click on the icon *to History*