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Usage of the UEB Server for external users

This page describes how to connect to the UEB Server for VHIR or external researchers that have contracted the usage of the UEB server for their own research in a self-service basis.

Page contents:


1. Service details

Basic service includes:

  • 200Gb of hard drive space
  • 3 days of usage included for free during the first service contracted.
  • 6 CPU from the UEB server ueb.vhir.org, or 8 from the ueb2.vhir.org, running GNU/Linux OS, 64bits, with 32 Gb RAM.
  • Usage of the following pre-installed programs:
    1. R (3.x) & RStudio
    2. CRAN and Bioconductor repository of packages
    3. installation of custom R packages as needed
    4. Stata (13.x)
    5. CLCBio (8.x)
    6. IGV (2.x)
    • For other software programs, contact the UEB.


Extra resources will be charged upon resource consumption on a pre-stablished fare per space and time consumed.

Contact the ueb@vhir.org for any doubt or question about the service.

1.1. Which UEB server is the one I need to connect to?

Some programs are restricted to one server due to licensing restrictions. Some others can be used in either one or the other. See this brief list below as orientation:

ueb.vhir.org ("B52"):

  • R + RStudio and similar (RCmd, AffylmGUI, OneChannelGUI, ...)
  • Stata
  • IPA
  • others (IGV, and other system programs)
ueb2.vhir.org ("Trompeta"):
  • R + RStudio and similar (RCmd, AffylmGUI, OneChannelGUI, ...)
  • CLC Genomics Workbench
  • IPA
  • others (IGV, and other system programs)

2. Login

How to login as an external user to the specific UEB server?
You need to install a local X2Go client

Quick guide

Using the X2Go Client for your Operating system. Get it from:
http://wiki.x2go.org/doku.php/doc:installation:x2goclient

You need to setup a connection to :

  • Name: UEB Server 1 or UEB Server 2
  • Server: ueb.vhir.org or ueb2.vhir.org
  • Session: LXDE
  • User: your-username-from-the-bookings-system
  • Password: your-password-from-the-bookings-system

2.1. Step by step instructions to install X2Go client

You need to install x2goclient in the client computer in order to connect to use most server programs.

In GNU/Linux

See: http://wiki.x2go.org/doku.php/doc:installation:x2goclient#ubuntu_debian and sections below for other distributions.

In short, you can use your package manager (apt-get, yum, or equivalent in your distribution) to install the x2goclient.

You can also do it through a console terminal, switching your user to root to install programs:

sudo apt-get install x2goclient


Do you want to add the repository with latest versions of the program?

Click to show/hide the extra information

If you want to add the repository to get the more updated versions of X2Go and you are at the VHIR network, or behind a Firewall, you need to export the proxy location first to your session, so that your computer knows how to reach the internet to fetch a new repository to add the X2Go client:

Commands run in a console terminal
sudo su
export http_proxy=http://conf_www.ir.vhebron.net:8081/
export https_proxy=http://conf_www.ir.vhebron.net:8081/
export ftp_proxy=http://conf_www.ir.vhebron.net:8081/


Then you can run these commands:

commands run as root
apt-get install python-software-properties
apt-add-repository ppa:x2go/stable
apt-get update
apt-get install x2goclient
exit


If you search for the X2Go program in your desktop enviornment and lanuch it from there, for instance (or from the Classic Menu: "Network > X2Go Client"):

Image



That should be it.

2.2. Set up Connection details

Launch the X2Go program in a similar way to what you do in your operating system for other programs, and click at the button to add a new connection (the first one in the horizontal bar at the top):

Click to enlarge
Click to enlarge


Set up the connection details, with all options with default but:

  • Session name: UEB Server 1 or UEB Server 2 (as you wish)
  • Host: ueb2.vhir.org (default option for accessing IPA) or ueb.vhir.org
  • Login: your-username-from-the-bookings-system (vhir in case of accessing IPA!!)
  • SSH Port: 22
  • Session type: LXDE
Click to enlarge
Click to enlarge


Once you attempt to use this connection, you will be shown your username as indicated before, and you will be required to type corresponding password for that user:

  • Login: your-username-from-the-bookings-system(or vhir in case of accessing IPA!!)
  • Password: your-password-from-the-bookings-system

Click to enlarge
Click to enlarge

2.3. Test the connection

Launch the program x2goclient, click at the name of the connection on the right, which will ask you for the password for that user you defined in the connection settings. Once connected, you will be shown very quickly that the connection is performed successfully. And a new window will open with the remote desktop inside (LXDE in this case):

Click to enlarge
Click to enlarge


You can now work normally at the chosen UEB server.

Once you have finished you have two options to logout:

  1. Close the session
  2. Close the window in order to leave the program while leaving the working session open for you, so thast you can continue later (provided that you have booked a long enough time frame for that re-connection later).


(1) If you want to close the session, click at the button at the horizontal panel from the server desktop similarly to the figure below:

Fes clic per ampliar
Fes clic per ampliar



(2) If you want to close the connection window but leave the work session open at the server (in order to continue working later at the same point where you left at that moment), go to the window of the working session from your local operating system, and close there the window. Your working session at the server will remain open.

Fes clic per ampliar
Fes clic per ampliar



That's it. Every time you need it, you can start a session again within your booked time, following the instructions above.

3. Transfer results from and to your local machine

3.1. Using SFTP


Upload your data files to the server, using some sftp program, such as FileZilla ( https://filezilla-project.org/download.php ), to access the ueb.vhir.org server.

3.1.A. Connection details with FILEZILLA
Connect using "Site manager > New Site":

  • host: ueb.vhir.org or ueb2.vhir.org
    • alternatively, you can use ip number instead, as shown in the screenshot below
  • server type: SFTP - SSH File Transfer Protocol
  • login type: Normal
  • user: your-username-from-the-bookings-system (or vhir for IPA)
  • password: your-passsword-from-the-bookings-system

Image

In "Edit > Parameters > Generic Proxy", you have to set up an intermediary proxy server as:
  • Generic Proxy Type: SOCKS 5
  • Generic Proxy Host: socks.ir.vhebron.net
  • Generic Proxy Port: 1080

Image
3.1.B. Connection details with WinSCP (only Windows)
Image
Connect using ...:
  • host: ueb.vhir.org or ueb2.vhir.org
    • alternatively, you can use ip number instead, as shown in the screenshot below
  • server type: SFTP - SSH File Transfer Protocol
  • login type: Normal
  • user: your-username-from-the-bookings-system (or vhir for IPA)
  • password: your-passsword-from-the-bookings-system

Click to enlarge
Click to enlarge


In the proxy settings, set it to use the system settings for the proxy. (and ensure that you have the proxy set up properly in you Windows )
Depending on the computer setup, you can also skip the proxy definition, and set to use none "Ninguno":

Click to enlarge
Click to enlarge


In case you are shown a screen to accept footprint the rsa2 server key (similar to this window), click at yes (Si) to accept:

Click to enlarge
Click to enlarge


Upload your data files to the server:

    • Create a folder with your name under /home/vhir/Desktop/Usuaris/ for IPA (since you all connected with user "vhir"), or in your home folder for other connections. You can use either of the programs FileZilla (multiplatform) or WinSCP (windows onlly) for that, or request the UEB to create that folder for you if you don't know how to do it or any issues from your computer arise.
    • Upload your files inside your own folder /home/vhir/Desktop/Usuaris/your_username/ for IPA (or /home/your_username/your_folder/ otherwise)


Once finished, transfer the results to your machine.

Delete your files from the server if you don't want others to see them.

3.2. Using HTTP (Downloading from Web pages)

Click to enlarge
Click to enlarge

If you need to fetch data files from external web pages (not available through ftp but only through http web pages), you can setup FoxySpider extension of the Mozilla Firefox browser, to indicate which type of files you want to download:

  1. Open the Mozilla Firefox browser and right click on the FoxySpider icon in the Mozilla Firefox toolbar.
  2. This will open the FoxySpider Preferences window
  3. Select the third tab: "Content"
  4. Adapt the checkboxes to select the types of files that you are interested in. In the associated screenshot, only files with extensions .bowtie and .fastq will be downloaded. Save your preferences



Then you can:

  1. Navigate to your the web page where you have the list of files you want to download in batch. Once in that page, click with the left button in your mouse over the FoxySpider icon.
  2. Wait until the webpage is loaded by FoxySpider
  3. Choose your desired method to select which files to download
  4. If you choose to select files manually, do so by means of Ctrol+Click over the files you are interested in.
  5. Finally, click at the "Download files" button.
    A dialogue will open asking where do you want to save the files to. Choose your folder under /home/vhir/Usuaris/youruser/.
  • You are done.
    Click to enlarge
    Click to enlarge



Once finished, transfer the results to your machine, through sftp as explained above.

Delete your files from the server if you don't want others to see them.

4. Check space used in the hard drive

You can check the amount of hard drive space that you are using, at anytime, by mean of running the following command in a terminal/console window:

youruser@ueb# du ~ -hs


For IPA sessions, replace yourusername with the username you use to store your data into for IPA sessions:

vhir@ueb# du /home/vhir/Desktop/yourusername/ -hs

5. Contact

Do not hesitate to contact us for questions or issues that you detect:

Phone. +34 93 489 4007
ueb@vhir.org
Edifici Mediterrània, Despatx 131 (1a planta)
UEB - Statistics and Bioinformàtics Unit
VHIR - Vall d'Hebron Research Institute