2 Managing files
Both Pod and Knot allow for 4 TB of file storage per user and more can be requested if needed. File management on the server clusters involves commonly used Linux commands to navigate and modify files and folders. The generic setup is
$ command [options] <arguments>Most of the following commands have multiple options that are not covered here. For detailed documentation enter the command man <command>. Additionally, for a broader introduction to Linux commands see the Software Carpentry’s lessons at http://swcarpentry.github.io/shell-novice/.
2.2 Viewing, creating, and editing files
file file.txt - view file type information
stat file.txt - view file information
more file.txt - view text file one screen at a time (to exit press q)
less file.txt - view text file with scrolling (to exit press q)
head file.csv - print first ten rows of text file
tail file.csv - print last ten rows of text file
head -1 file.csv - print column names if in first row of text file
cut -d , -f 2,4-6 file.csv | less - view specific columns of CSV file by number position (e.g., 2,4-6)
To view CSV files with pretty output, enter
cat file.csv | sed -e 's/,,/, ,/g' | column -s, -t | less -#5 -N -S
Note: This may not work well for all files. Use arrow keys to navigate and press q to exit.
cat > file.txt - create new text file (to save and exit press Ctrl+D)
nano - create new text file using nano text editor
nano file.txt - view and edit text file using nano text editor
zip -r file.zip file1 folder1 - create compressed ZIP file with recursion
unzip file.zip - extract ZIP file into working directory
2.3 Permissions
Sometimes file and folder permissions need to be modified, such as to restrict access to files. On Linux, read, write, and execute permissions are represented by octal notation and applied to the file owner, groups, and all other users.
| # | Permission | rwx |
|---|---|---|
| 7 | read, write, and execute | rwx |
| 6 | read and write | rw- |
| 5 | read and execute | r-x |
| 4 | read only | r– |
| 3 | write and execute | -wx |
| 2 | write only | -w- |
| 1 | execute only | –x |
| 0 | none | — |
Common permissions include
-rwxrwx--- = 770 - owner and group can do everything, but others can do nothing
-rwxr-x--- = 750 - owner can do everything, group can read and execute only, but others can do nothing
-rwx------ = 700 - owner can do everything, but group and others can do nothing
To change permissions enter
chmod 770 dir - change permissions for file or directory
chmod -R 770 dir - change permissions recursively for directory
chgrp group file - change group ownership for file or directory
2.4 Shortcuts
Ctrl+A - move to beginning of line
Ctrl+E - move to end of line
Ctrl+U - clear line from cursor
Ctrl+C - cancel command
~ - home directory
. - current directory
.. - one directory up
* - wildcard completion
Tab key - autocompletion
Up and down arrow keys - cycle through command history