Remote access and file transfer
Logging in from another machine
Getting files on and off Bio-Linux
Overview
Remote logins to Bio-Linux with ssh Running software from another machine
Transferring files to and from a Bio-Linux machine Networked file systems and file-sharing
Removable media (floppies and CDs) Backing up your data
Logging in remotely
To log in to your Bio-Linux machine from another machine, you need to use a Secure Shell (SSH) program.
Secure Shell looks like telnet, but is secure - it uses encryption.
How you access Bio-Linux remotely using SSH depends on what system you are logging in from.
SSH clients by platform
Windows: We recommend PuTTY (
http://www.chiark.greenend.org.uk/~sgtatham/putty/). It is a free, lightweight and capable SSH client.
Mac Classic: MacSSH (http://pro.wanadoo.fr/chombier/)
Mac OSX: Built in ssh at the command line
Linux/Unix: OpenSSH (http://openssh.org) is the Open Source ssh suite. It is installed on Bio-Linux by default.
Running graphical programs
remotely
You can run graphical programs remotely.
If you want to launch graphical applications when logged in via ssh you will need to enable “X11 forwarding”
You also need an 'X server' running on the local machine. For Windows, this probably means the Exceed package.
Running the full desktop
remotely
What if you want a full Bio-Linux desktop to work with remotely?
Simple: Just log in via SSH with X11 forwarding turned on and type the following command:
gnome-session &
You will get a full interactive Gnome desktop on your machine! It will be just like being on the Bio-Linux machine (but slightly slower!)
Working via SSH - summary
Configuring a graphical SSH client is very easy You will need a username
The IP address and/or hostname of the machine
Some clients make you specify the SSH port (22 by default) If you want to use graphical applications over the ssh
“tunnel” you will need to enable “X11 forwarding”, and have an “X server” running on the local machine.
Command line SSH basics
Logging into a machine using a SSH client from the command line is easy:
To make sure X forwarding is turned on with OpenSSH ssh -X [email protected]
(But the ssh on Bio-Linux does this by default)
Getting data from remote
machines - FTP
Most likely you are familiar with FTP, eg. for downloading files off the Web.
Mozilla can retrieve files from public FTP sites – this is known as “anonymous FTP”.
gFTP is a good graphical FTP client which is part of the GNOME desktop.
Getting data from remote
machines - FTP
Bio-Linux also has a command line FTP client.
At a terminal type:
ftp <hostname>
You will be prompted for a username and password.
You can also use “wget” to retrieve files with a single command
wget ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release/sprot42.dat wget http://envgen.nox.ac.uk/envgen/training/archives/intro_to_linux.pdf
sFTP
If the server supports it you should use sftp
instead of FTP.
sFTP = secure FTP
sftp <username>@<hostname>
The rest of the commands are just like FTP
Relies on sshd.
SCP
scp also copies files between machines
scp <filename> <username>@<host>:<dir> scp myfile.txt [email protected]:docs
Great for shunting single files around
between Linux machines.
This is a secure way to transfer files.
WinSCP
For getting files from Windows to Bio-Linux there is a great (free!) program called WinSCP
It looks just like a regular windows file manager.
You can “drag and drop” files to and from your Bio-Linux machine.
Handles SCP and SFTP transparently
Using networked file stores
You may have shared drives at your place of work. These may be NOVELL shares – A novell client is available for Linux so you can access these. smbclient : allows you to access Windows Shares NFS : Bio-Linux can be easily set up to connect NFS shared drives.
Ask us for advice on all of these!
Removable media
Bio-Linux reads 'regular' windows floppies – see the FAQ for more details.
You can write CDs – use GCombust.
CD-R – cheap – write-once – very compatible
CD-RW – cheapish – not compatible with older drives
Zip – buy a USB drive if needed
Backing Up Data
The EGTDC cannot be held responsible for any loss of data on the Bio-Linux machines, be it from user error, hardware failure or software failure.
Users are responsible for their own data
The nominated system administrator should ensure all users of the system backup their data.
Talk to your local support staff, and make use of networked backup facilities.
Looking after your /home
Save your files to a floppy disk, if they fit, or else a CD.
Save files to networked file stores.
Use “tar” and “bzip2” to compress your files into archives, saving space.
Save backup copies of files in your home directory in case of accidental deletion.
Disaster recovery on Bio-Linux
There is a built-in backup system in Bio-Linux. Once daily, an image of the primary hard drive is stored on the secondary disk.
This is designed for disaster recovery in the case of hard disk failure, not for recovering individual files. The advanced course has more information.
