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Main commands in marbec-gpu Terminal

The first thing to keep in mind is that marbec-gpu has Ubuntu installed, so the commands listed below will be the same as the ones used in that OS. This article will show a description of the main usage modes for each command, but if you have any additional requirements, you can always search in forums like Stackoverflow or check the help for each command, which consists of placing the command name followed by --help. For example, if I want to know the help for the ls command, just run ls --help in the Terminal.

Upper and lower case

As in R or Python, the use of upper or lower case when indicating an option does matter. For example, ls -D is not equivalent to ls -d, so be carefull.

Browsing within folders

• Command: cd
• Usage: cd path/folder

To indicate a previous position (folder), you will use the statement .. as follows: ../path/folder1 (this indicates that there is a folder called path from the folder where you are, and that that has a folder called folder1 as well).

Create a folder

• Command: mkdir
• Usage: mkdir path/folder

Get the content of a folder as a list

• Command: ls
• Usage: ls path/folder/

Main options:

• --all (o -a): Displays all files and subfolders, including those protected (hidden) by the system.

Generate a list of files/folders and display the size of each item

• Command: du
• Usage: du path/to/file.csv o du path/to/folder

Main options:

• --human-readable (o -h): changes the units dynamically to avoid displaying all Kb. This is especially useful when you have large objects (subfolders or files).

• --summary (o -s): displays a summary table, i.e. it only includes the subfolders and files present at the first search level. This is useful when we just want to take a quick look and avoid displaying a complete listing of ALL internal subfolders.

If I want to get a list of all the files and folders inside a folder with their respective sizes (the three options are equivalent):

du ruta/de/folder/* --human-readable --summarize
du ruta/de/folder/* -h -s
du ruta/de/folder/* -hs

Copy-paste

For this, the simplest way is through the cp command and making use of the navigation commands cited in this post (e.g. .. to indicate a previous folder). The basic syntax is the following: cp path/origin /path/destination, but there are different possible cases:

• Copy a file into the same folder, but with a different name (create duplicate): cp file1.csv file1-dup.csv.

• Copy a file to another folder: cp path/file1.csv path/destination.

• Copy more than one file to another folder: cp path/file1.csv path/file2.csv folder/destination

• Copy a folder to another folder: cp path/folder1 path/folder2 --recursive or cp path/folder1 path/folder2 -r.

Note

By default, cp will overwrite any file with the same name. To avoid this, it is possible to add the -n option as follows: cp path/from/file1.csv path/destination -n.

Cut-paste (and also rename)

It will be very similar to the above, but through the mv command:

• Rename a file (within the same folder): mv file1.csv file2.csv

• Move a file to another folder: mv path/file1.csv path/to/destination

• Move one file to another folder: mv path/file1.csv path/file2.csv path/destination

• Move one folder to another folder: mv path/old/folder path/new/folder

Delete

For this, we will use the rm command as follows:

• Delete a file: rm path/to/file.csv

• Delete a folder (and all its contents): rm path/to/folder -r

No turning back

While inside Terminal it is always possible to cancel a command using the shortcut Ctrl+C (or Cmd+C on MacOS), once the rm command completes its work, there is no way to revert the deletion or recover it from a recycle garbage can, so be very careful when using it.

Display current processes

• Command: top

When you run it, it will show in interactive mode in Terminal the processes that are running, as well as the resources used by each of them (basically like a Task Manager). To exit this interactive mode, just press the q key.

Stop a process

If we want to force the closing or the cancellation of a process already started, we can use the shortcut Ctrl+C (or Cmd+C in MacOS). It is important to keep in mind that forcing the closing of a process that had in progress the handling of files or folders (creation, copy, etc.) can leave the generated files unusable.

Viewing a plain text file

By default, there are two tools available from Terminal: vi and nano. The syntax for their execution is as simple as vi path/file1.txt or nano path/file1.txt, where file1.txt can be any plain text file (e.g. an R or Python script). The navigation shortcuts within each of these environments are different, but documentation is abundant on the Internet. Choose the one you like best.