Copying files and directories locally and remotely

Copying files and directories cp

cp file1 file2 is the command which makes a copy of file1 in the current working directory and calls it file2.

Let's copy our first touch file and name it same but with adding "_copy" (P.S. don't forget to use Tab to auto-complete long names of our files):

cp my_first_touch_file.txt my_first_touch_file_copy.txt

Now when we learned how to cp files, let's copy the exercise directory from /opt/evop/public/BIOINFORMATICS/unix_intro/exercises to your home directory (~). We can copy a directory and all its contents by using the recursive option -r:

cp -r /opt/evop/public/BIOINFORMATICS/unix_intro ~

To make sure the files are copied correctly, we can type ls unix_intro

Often we would need to copy several files at once. This can be done by providing a list of individual filenames followed by a directory name where to copy those files (i.e. cp [file1] [file2] ... [Dir where to copy]).

For this exercise, let's make a directory called backup. Now let's copy files from ~/unix_intro/exercises/ called 1_browsing_textfiles.txt and 2_searching_patterns.txt in it.

cd
mkdir backup
cp ~/unix_intro/exercises/1_browsing_textfiles.txt ~/unix_intro/exercises/2_searching_patterns.txt backup

Secure copy (remote file copy program) scp

The files we copied are still in our directories at the FU cluster. We can copy files and directories to our local machines using scp command (secure copy). The scp is a remote file copy program that allows us to securely copy files and directories between remote hosts without starting an FTP session or logging into the remote systems explicitly.

The syntax for the scp command is:

scp [options] username1@source_host:directory1/filename1 username2@destination_host:directory2/filename2

The location of the source file is specified by username1@source_host:directory1/filename1, which includes the:

• Name of the account on the host computer (username1)
• A hostname of the computer on which the source file resides (source_host)
• Name of the directory containing the source file (directory1)
• A filename of the source file (filename1)

The location to which the source file will be copied is specified by username2@destination_host:directory2/filename2, which includes the:

• Name of the account on the destination computer (username2)
• A hostname of the computer to which the source file will be copied (destination_host)
• Name of the directory to which the source file will be copied (directory2)
• A filename of the copy (filename2)

The tricky part here is that we need to do it in two steps (in reverse compared to the login process):

1. First step is copying from evop-login to andorra. Let's try it, open a new terminal session from your local machine, log in to andorra, and then copy the unix_intro directory from evop-login to the current directory while being logged-in to andorra:

ssh YourID@andorra.imp.fu-berlin.de # enter your password once asked for it
scp -r evop-login:~/unix_intro .

1. Second step is copying it from andorra to our local machines. To do so, open a new terminal session from your local machine go to a directory where you wanna save your files (e.g. Downloads), and then copy the unix_intro directory from andorra using scp:

scp -r YourID@andorra.imp.fu-berlin.de:~/unix_intro . # enter your password once asked for it

Please note that here we are using our current directory (.) at our local computers as the location to which the file will be copied, and since we are already logged-in to our computers we do not need to print the entire paths such as username2@destination_host:directory2/filename2.

WinSCP for Windows

In case we want to copy our files to a Windows machine, without using the command-line, we can do it using WinSCP. Login is very similar to the one used with Putty. Once logged-in into the server, you will see WinSCP split into two windows. Left (your PC) Right (the server). Just move the contains from right to left and vice-versa using the mouse.