How to move data between Galaxy and another computer system?
There are several secured methods to use. Examples are scp,
sftp, and passive ftp.
Using "scp", you can use be very flexible in moving data
from one computer system to another. For example, if you
want to copy files from the system where you issue the
command to a remote destination system, you may use the command
% scp filename user@remotehost:/dest/dir/for/file/
An example of this would be when you copy your files from
Galaxy to an AMS computer, such as poincare. In that case,
you can issue the command on starzero:
% scp filename user@poincare:/dest/dir/for/file/
You may also copy a directory recursively, using the option
"-r", for example,
% scp -r a_directory user@poincare:/dest/dir/
Of course, using "scp" you can also copy files from a
remote system to the computer you are logged in. The command
would be
% scp user@remotehost:/dir/remotefile /dest/dir/file
Another powerful tool for file transfer is "sftp". Not only
"sftp" is secure, it is also much more convenient due to its
recursive transfer of directories. On the machine where you
are logged in (such as Galaxy), just issuing the command
% sftp remote_host
will establish the connection. Then, if you use the sftp
command
sftp> get a_directory
you will get all the files under the direcotry recusively.
The sftp commands are very similar to the conventional
"ftp". The only thing one should pay particular attention to
is that "sftp" must be connected to a machine which is
running ssh2 service. Currently, on the AMS network, the
machine "stoker" is installed by the Galaxy staff, and it is
know to be sure running ssh2. You can certainly sftp to that
machine to or from Galaxy.
Though it is not encrypted, the old "ftp" protocal can still
be used to transfre data to and from Galaxy, but it must be
in "passive" mode in order to garantee security. So, once
the ftp connection is established, the first command to use
must be "passive". Only after that, the data transfer can
be conducted.