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Upload Data in Galaxy@Pasteur

Olivia Doppelt-Azeroual, Fabien Mareuil

1 / 7

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:
    sftp -P 2222 yourlogin@galaxy.pasteur.fr
    or
    sftp -oPort=2222 yourlogin@galaxy.pasteur.fr
  • Remark if data are on tars, first connect to it (with your pasteurID password):
    ssh yourlogin@tars.pasteur.fr
    REMARK: Use the galaxy password for the sftp connection
2 / 7

Upload a data if size is > 2Go (command line) (2/2)

Command line (Terminal) solution

  • To upload a file on the sftp server:
    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:
      sftp>mkdir mydirectory
      sftp>put -r mydirectory
3 / 7

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
4 / 7

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
5 / 7

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
  • It's possible to create folder to organize your data
  • To upload file you transfered in your link directory (from User Directory):
6 / 7

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

  • Then select your data and click on the icon to History

7 / 7

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:
    sftp -P 2222 yourlogin@galaxy.pasteur.fr
    or
    sftp -oPort=2222 yourlogin@galaxy.pasteur.fr
  • Remark if data are on tars, first connect to it (with your pasteurID password):
    ssh yourlogin@tars.pasteur.fr
    REMARK: Use the galaxy password for the sftp connection
2 / 7
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