C2110 UNIX and programming Lesson 2 / Module 4 -1C2110
UNIX and programming
Petr Kulhanek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
Lesson 2 / Module 4
PS / 2020 Distance form of teaching: Rev1
C2110 UNIX and programming Lesson 2 / Module 4 -2Remote
File Transfer
➢ scp (rsync)
➢ wget (curl)
➢ Data Transfer Between Unix/macOS OS and MS
Windows (WinSCP)
C2110 UNIX and programming Lesson 2 / Module 4 -3Remote
Copying
$ scp [-r] source target
Examples of use:
Syntax:
[] - can be omitted
Source and target can be a file or a directory. When copying directories, the option -r
(recursive) must be used.
The remote destination or host is identified by the machine name separated from the file
or directory name by a colon.
[user@]hostname:[/path/]file
$ scp test.txt wolf01.ncbr.muni.cz:/scratch/kulhanek
$ scp wolf01.ncbr.muni.cz:/scratch/kulhanek/test.txt .
Use the command scp for remote copying.
The command more convenient for copying a larger amount of
data (directory synchronization) is rsync (C2115).
C2110 UNIX and programming Lesson 2 / Module 4 -4Exercise
1
1. Make a copy of the directory ~/Documents/ C2110 to the directory /scratch/username
(make sure you have some files in the directory ~ /Documents/C2110, e.g., a
presentations for exercises).
2. Copy the contents of the directory /scratch/username/Documents to the remote
machine of your choice into the directory /scratch/username/wolfXX, where wolfXX is
the number of the source machine. Use the command to scp.
3. Delete directories /scratch/username/Documents and /scratch/username/wolfXX
use two terminals
username - your username
C2110 UNIX and programming Lesson 2 / Module 4 -5Downloading
Files from the Web
You can use the command wget to download files from the web. Remote machines must
provide files using a ftp, http or https protocol.
$ wget [-O output_name] url
url (uniform resource locator)
www file identifier
Examples of use:
$ wget http://www.rcsb.org/pdb/files/1SS9.pdb
PDB code structure
big O
A similar command is curl. However, it allows two-way communication with a
remote machine.
C2110 UNIX and programming Lesson 2 / Module 4 -6Exercise
2
1. Use the wget command to download the 1SS9 PDB structure to a file named
structure.pdb and save it to a directory ~/Documents/C2110
2. Download the installation image using the wget command (iso file) for Ubuntu Server
18.04 to the directory /scratch/username. Verify its checksum by command md5sum
or sha256sum.
3. Delete the installation image.
username - your username
C2110 UNIX and programming Lesson 2 / Module 4 -7Data
Transfer MS Windows <> UNIX
Text files created under MS Windows and Linux (macOS) are not completely compatible
because each operating system uses a different encoding for end of line.
Linux (macOS): \n (line feed 0x0A)
MS Windows: \r+\n (carriage return 0x0D, line feed 0x0A)
For coding conversion, see C2110-CZ-MSWindows-M01.pdf
C2110 UNIX and programming Lesson 2 / Module 4 -8-
Homework
C2110 UNIX and programming Lesson 2 / Module 4 -9-
Homework
1. Download the presentation from the directory
/home/kulhanek/Documents/C2110/Presentations to your computer with WinSCP or
scp commands. Presentations are available in the format pdf and commented
presentations in mkv format (video).