Logging into COLA Computers

Overview

Teaching: 0 min
Exercises: 0 min

Questions

Why do I need to login to another computer?

How do I login to COLA computers?

Objectives

Explain why it is necessary to login to another computer

Explain what computer systems exist at COLA to log into

Explain how to login to the COLA computers from a learner’s computer

In atmosphere, ocean, and climate science most of our data analysis work is done on Unix or Linux computers. These types of computers have more computational capability, more memory, and more disk (or hard drive) space than a personal computer. We need this to handle the many large datasets used in climate data analysis.
COLA computers already contain many of the datasets we will work with. These datasets are too large for your home computer and would take weeks to months to download.
Unix computers use a command line interface that allow us to automate our data processing tasks much faster than a graphical user interface (GUI).

COLA Computers

The Center for Ocean-Land-Atmosphere Studies (COLA) in the Department of Atmospheric, Oceanic, and Earth Sciences (AOES) has Linux computers used to analysis of Climate Data. They consist of cola1, cola2, cola3, … , cola7. These are the computers we will use in this class.

Setting up Software for your computer

To login to the COLA computers, you need secure shell (ssh) software. The software differs based on what type of computer you have.

macOS

For a Mac computer, use software called Xquartz

Windows

For a Windows computer, use software called MobusXterm

Linux

The default Unix Shell for Linux operating systems is usually Bash. On most versions of Linux, it is accessible by running the (Gnome) Terminal or (KDE) Konsole or xterm, which can be found via the applications menu or the search bar. If your machine is set up to use something other than Bash, you can run it by opening a terminal and typing bash.

Download and install the correct ssh software for your computer

Download the correct software for your computer

Follow the instructions on your computer to install the software

In this class, you can

Raise your hand when you need assistance or have a question

Indicate you are done with an activity in the colaborative document

Logging in

If you do not already have a COLA account, I will provide you with your username and password in class.

On macOS

Launch the XQuartz software you downloaded and select Shell-> New Window from the menu in the upper left. A window will appear that looks something like (look may vary depending on version of macOS and/or some default settings in Xquartz):

XQuartz window

To connect to the computer cola1 , type the following and replace username with your username:

$ ssh -Y -l username@cola1.gmu.edu

Enter your password when prompted. You will now be required to change your password.

On Windows

Launch the MobusXterm software you downloaded.
Click Session->SSH
In the Remote host box, enter cola1.gmu.edu
Check the Specify username box and enter your username
Click OK
Enter your password when prompted
Select No when asked to save your password.

You will now be required to change your password. Follow the prompts change your password.

Password Requirements & Policies

-Password complexity requirements will be provided in class.

-Keep your password secure and in a safe place

-Do not share your password.

-No one will every ask you for your password. If you ever get an email asking for your password DO NOT respond to it, it is a phishing attempt.

-Do not store your password in plain text.

-Passwords must be changed every 6-months

-Follow the Mason Responsible Use of Technology Policies

Login to a different COLA computer

COLA computers are cola1, cola2, cola3, … , cola7

Choose a computer other than cola1 and login to it.

Key Points

You need to use COLA computers for this class

COLA computers that you can log into are cola1-7

Secure (ssh) software is used to login to COLA computers

Shell Commands

Overview

Teaching: 0 min
Exercises: 0 min

Questions

How do I use the Unix shell?

Objectives

Introduce Unix Commands, switches, and how to get more info

Background

Now that you have logged into the COLA computers, the computer is waiting for you to tell it what to do. In this class, we will also work on the NCAR supercomputer. Both use the Unix shell to receive commands telling the computer what to do.

The Shell

The shell is a program where users can type commands. With the shell, it’s possible to invoke complicated programs like climate modeling software or simple commands that create an empty directory with only one line of code. The most popular Unix shell is Bash (the Bourne Again SHell — so-called because it’s derived from a shell written by Stephen Bourne). Bash is the default shell on most modern implementations of Unix and in most packages that provide Unix-like tools for Windows.

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

The shell typically uses $ as the prompt, but may use a different symbol. In the examples for this lesson, we’ll show the prompt as $ . Most importantly: when typing commands, either from these lessons or from other sources, do not type the prompt, only the commands that follow it.

Most of you (80%) indicated in the Pre-Course Survey that you use the Unix shell daily or weekly. I have found in previous classes than many times students know a small set of basic commands, but very few useful options or switches and are not familiar with commands that can greatly help your work and the work we will need to do to run Earth System Models on a super computer. Therefore, we will review some Unix basics here and you will review some additional helpful command on your own prior to next class.

ls means list the contents of the directory I am in

$ ls

$ ls -F /

ls is the command, with an option -F (also called switches or flags) and an argument /.

Unix commands have many options that are very useful. Let’s look at some for ls

Exploring More ls Flags

You can also use two options at the same time. What does the command ls do when used with the -l option? What about if you use both the -l and the -h option?

Some of its output is about properties that we do not cover in this lesson (such as file permissions and ownership), but the rest should be useful nevertheless.

Solution

The -l option makes ls use a long listing format, showing not only the file/directory names but also additional information such as the file size and the time of its last modification. If you use both the -h option and the -l option, this makes the file size ‘human readable’, i.e. displaying something like 5.3K instead of 5369.

Listing in Reverse Chronological Order

By default ls lists the contents of a directory in alphabetical order by name. The command ls -t lists items by time of last change instead of alphabetically. The command ls -r lists the contents of a directory in reverse order. Which file is displayed last when you combine the -t and -r flags? Hint: You may need to use the -l flag to see the last changed dates.

Solution

The most recently changed file is listed last when using -rt. This can be very useful for finding your most recent edits or checking to see if a new output file was written.

Getting help

ls has lots of other options. There are two common ways to find out how to use a command and what options it accepts:

We can pass a --help option to the command, such as:
```
 $ ls --help
```
We can read its manual with man, such as:
```
 $ man ls
```

Key Points

Unix commands consist of the command, options or switches, and input to the command

Additional switches can be found using man or --help

Navigating Files and Directories

Overview

Teaching: 0 min
Exercises: 0 min

Questions

How can I move around on my computer?

How can I see what files and directories I have?

How can I specify the location of a file or directory on my computer?

Objectives

Explain the similarities and differences between a file and a directory.

Translate an absolute path into a relative path and vice versa.

Construct absolute and relative paths that identify specific files and directories.

Use options and arguments to change the behaviour of a shell command

Demonstrate the use of tab completion, and explain its advantages.

The part of the operating system responsible for managing files and directories is called the file system. It organizes our data into files, which hold information, and directories (also called ‘folders’), which hold files or other directories.

Several commands are frequently used to create, inspect, rename, and delete files and directories. To start exploring them, we’ll go to our open shell window.

First let’s find out where we are by running a command called pwd (which stands for ‘print working directory’). Directories are like places - at any time while we are using the shell we are in exactly one place, called our current working directory. Commands mostly read and write files in the current working directory, i.e. ‘here’, so knowing where you are before running a command is important. pwd shows you where you are:

$ pwd

Moving around files and directories

$ cd

$ cd ..

.. is a special directory name meaning “the directory containing this one”, or more succinctly, the parent of the current directory.

The basic commands for navigating the filesystem on your computer: pwd, ls and cd. Let’s explore some variations on those commands.

What happens if you type cd on its own, without giving a directory?

$ cd

How can you check what happened? pwd gives us the answer! It turns out that cd without an argument will return you to your home directory, which is great if you’ve gotten lost in your own filesystem.

$ pwd

/homes/kpegion

Let’s get some data and examples to work with for this lesson:

First, copy the file /homes/kpegion/classes/fa2020/data-shell.zip to your home directory

$ cd
$ cp /homes/kpegion/classes/fa2020/data-shell.zip .

Unizp the file:

$ unzip data-shell.zip

Let’s go explore the directories we copied:

$ cd data-shell/data

Check that we’ve moved to the right place by running pwd and ls -F

Here we used the relative path to specify the directory. When you use a relative path with a command like ls or cd, it tries to find that location from where we are, rather than from the root of the file system.

However, it is possible to specify the absolute path to a directory by including its entire path from the root directory, which is indicated by a leading slash. The leading / tells the computer to follow the path from the root of the file system, so it always refers to exactly one directory, no matter where we are when we run the command.

This allows us to move to our data-shell directory from anywhere on the filesystem (including from inside data). To find the absolute path we’re looking for, we can use pwd and then extract the piece we need to move to data-shell.

$ pwd

/homes/kpegion/data-shell/data

$ cd /homes/kpegion/data-shell

Run pwd and ls -F to ensure that we’re in the directory we expect.

Two More Shortcuts

The shell interprets the character ~ (tilde) at the start of a path to mean “the current user’s home directory”. For example, if Nelle’s home directory is /homes/nelle, then ~/data is equivalent to /homes/nelle/data. This only works if it is the first character in the path: here/there/~/elsewhere is not here/there/homes/nelle/elsewhere.

Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in, which is faster than having to remember, then type, the full path. This is a very efficient way of moving back and forth between directories. The difference between cd .. and cd - is that the former brings you up, while the latter brings you back. You can think of it as the Last Channel button on a TV remote.

Absolute vs Relative Paths

Starting from /homes/amanda/data, which of the following commands could Amanda use to navigate to her home directory, which is /homes/amanda?

cd .

cd /

cd /homes/amanda

cd ../..

cd ~

cd home

cd ~/data/..

cd

cd ..

Solution

No: . stands for the current directory.

No: / stands for the root directory.

No: Amanda’s home directory is /homes/amanda.

No: this goes up two levels, i.e. ends in /homes.

Yes: ~ stands for the user’s home directory, in this case /homes/amanda.

No: this would navigate into a directory homes in the current directory if it exists.

Yes: unnecessarily complicated, but correct.

Yes: shortcut to go back to the user’s home directory.

Yes: goes up one level.

Key Points

The file system is responsible for managing information on the disk.

Information is stored in files, which are stored in directories (folders).

Directories can also store other directories, which forms a directory tree.

cd path changes the current working directory.

ls path prints a listing of a specific file or directory; ls on its own lists the current working directory.

pwd prints the user’s current working directory.

/ on its own is the root directory of the whole file system.

A relative path specifies a location starting from the current location.

An absolute path specifies a location from the root of the file system.

Directory names in a path are separated with / on Unix, but \ on Windows.

.. means ‘the directory above the current one’; . on its own means ‘the current directory’.

Working With Files and Directories

Overview

Teaching: 0 min
Exercises: 0 min

Questions

How can I create, copy, and delete files and directories?

How can I edit files?

Objectives

Create a directory hierarchy that matches a given diagram.

Create files in that hierarchy using an editor or by copying and renaming existing files.

Delete, copy and move specified files and/or directories.

Creating directories

We now know how to explore files and directories, but how do we create them in the first place?

Step one: see where we are and what we already have

Let’s go back to our data-shell directory on the Desktop and use ls -F to see what it contains:

$ pwd

/homes/kpegion/data-shell

$ ls -F

creatures/  data/  molecules/  north-pacific-gyre/  notes.txt  pizza.cfg  solar.pdf  writing/

Create a directory

Let’s create a new directory called thesis using the command mkdir thesis (which has no output):

$ mkdir thesis

As you might guess from its name, mkdir means ‘make directory’. Since thesis is a relative path (i.e., does not have a leading slash, like /what/ever/thesis), the new directory is created in the current working directory:

$ ls -F

creatures/  data/  molecules/  north-pacific-gyre/  notes.txt  pizza.cfg  solar.pdf  thesis/  writing/

Good names for files and directories

Complicated names of files and directories can make your life painful when working on the command line. Here we provide a few useful tips for the names of your files.

Don’t use spaces.

Spaces can make a name more meaningful, but since spaces are used to separate arguments on the command line it is better to avoid them in names of files and directories. You can use - or _ instead (e.g. north-pacific-gyre/ rather than north pacific gyre/).

Don’t begin the name with - (dash).

Commands treat names starting with - as options.

Stick with letters, numbers, . (period or ‘full stop’), - (dash) and _ (underscore).

Many other characters have special meanings on the command line. We will learn about some of these during this lesson. There are special characters that can cause your command to not work as expected and can even result in data loss.

If you need to refer to names of files or directories that have spaces or other special characters, you should surround the name in quotes ("").

Since we’ve just created the thesis directory, there’s nothing in it yet:

$ ls -F thesis

Creating A File
$ touch my_file.txt
What did the touch command do?

Use ls -l to inspect the files. How large is my_file.txt?

Solution

The touch command generates a new file called my_file.txt in your current directory.

When you inspect the file with ls -l, note that the size of my_file.txt is 0 bytes. In other words, it contains no data. If you open my_file.txt using your text editor it is blank.

Moving files and directories

Returning to the data-shell directory,

cd ~/data-shell/

Let’s create a file called draft.txt in our thesis directory using a text editor:

$ vi thesis/draft.txt

Let’s type a few lines. First, type the i character (this stands for insert)

It's not "publish or perish" any more,
it's "share and thrive"

To save the file using this editor, use the esc key and then type ZZ

In our thesis directory we now have a file draft.txt that contains a quote. This is not a particularly informative name, so let’s change the file’s name using mv, which is short for ‘move’:

$ mv thesis/draft.txt thesis/quotes.txt

The first argument tells mv what we’re ‘moving’, while the second is where it’s to go. In this case, we’re moving thesis/draft.txt to thesis/quotes.txt, which has the same effect as renaming the file. Sure enough, ls shows us that thesis now contains one file called quotes.txt:

$ ls thesis

quotes.txt

One has to be careful when specifying the target file name, since mv will silently overwrite any existing file with the same name, which could lead to data loss. An additional option, mv -i (or mv --interactive), can be used to make mv ask you for confirmation before overwriting.

Note that mv also works on directories.

Let’s move quotes.txt into the current working directory. We use mv once again, but this time we’ll use just the name of a directory as the second argument to tell mv that we want to keep the filename, but put the file somewhere new. (This is why the command is called ‘move’.) In this case, the directory name we use is the special directory name . that we mentioned earlier.

$ mv thesis/quotes.txt .

The effect is to move the file from the directory it was in to the current working directory. ls now shows us that thesis is empty:

$ ls thesis

Further, ls with a filename or directory name as an argument only lists that file or directory. We can use this to see that quotes.txt is still in our current directory:

$ ls quotes.txt

quotes.txt

Moving Files to a new folder

After running the following commands, Jamie realizes that she put the files sucrose.dat and maltose.dat into the wrong folder. The files should have been placed in the raw folder.
$ ls -F
 analyzed/ raw/
$ ls -F analyzed
fructose.dat glucose.dat maltose.dat sucrose.dat
$ cd analyzed
Fill in the blanks to move these files to the raw/ folder (i.e. the one she forgot to put them in)
$ mv sucrose.dat maltose.dat ____/____
Solution
$ mv sucrose.dat maltose.dat ../raw
Recall that .. refers to the parent directory (i.e. one above the current directory) and that . refers to the current directory.

Copying files and directories

The cp command works very much like mv, except it copies a file instead of moving it. We can check that it did the right thing using ls with two paths as arguments — like most Unix commands, ls can be given multiple paths at once:

$ cp quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt

quotes.txt   thesis/quotations.txt

We can also copy a directory and all its contents by using the recursive option -r, e.g. to back up a directory:

$ cp -r thesis thesis_backup

We can check the result by listing the contents of both the thesis and thesis_backup directory:

$ ls thesis thesis_backup

thesis:
quotations.txt

thesis_backup:
quotations.txt

Renaming Files

Suppose that you created a plain-text file in your current directory to contain a list of the statistical tests you will need to do to analyze your data, and named it: statstics.txt

After creating and saving this file you realize you misspelled the filename! You want to correct the mistake, which of the following commands could you use to do so?

cp statstics.txt statistics.txt

mv statstics.txt statistics.txt

mv statstics.txt .

cp statstics.txt .

Solution

No. While this would create a file with the correct name, the incorrectly named file still exists in the directory and would need to be deleted.

Yes, this would work to rename the file.

No, the period(.) indicates where to move the file, but does not provide a new file name; identical file names cannot be created.

No, the period(.) indicates where to copy the file, but does not provide a new file name; identical file names cannot be created.

Moving and Copying

What is the output of the closing ls command in the sequence shown below?
$ pwd
/homes/jamie/data
$ ls
proteins.dat
$ mkdir recombine
$ mv proteins.dat recombine/
$ cp recombine/proteins.dat ../proteins-saved.dat
$ ls
proteins-saved.dat recombine

recombine

proteins.dat recombine

proteins-saved.dat

Solution

We start in the /homes/jamie/data directory, and create a new folder called recombine. The second line moves (mv) the file proteins.dat to the new folder (recombine). The third line makes a copy of the file we just moved. The tricky part here is where the file was copied to. Recall that .. means ‘go up a level’, so the copied file is now in /homes.jamie. Notice that .. is interpreted with respect to the current working directory, not with respect to the location of the file being copied. So, the only thing that will show using ls (in /homes/jamie/data) is the recombine folder.

No, see explanation above. proteins-saved.dat is located at /homes/jamie

Yes

No, see explanation above. proteins.dat is located at /homes/jamie/data/recombine

No, see explanation above. proteins-saved.dat is located at /homes/jamie

Removing files and directories

Returning to the data-shell directory, let’s tidy up this directory by removing the quotes.txt file we created. The Unix command we’ll use for this is rm (short for ‘remove’):

$ rm quotes.txt

We can confirm the file has gone using ls:

$ ls quotes.txt

ls: cannot access 'quotes.txt': No such file or directory

Deleting Is Forever

The Unix shell doesn’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do). Instead, when we delete files, they are unlinked from the file system so that their storage space on disk can be recycled. Tools for finding and recovering deleted files do exist, but there’s no guarantee they’ll work in any particular situation, since the computer may recycle the file’s disk space right away.

Using rm Safely

What happens when we execute rm -i thesis_backup/quotations.txt? Why would we want this protection when using rm?
Solution
$ rm: remove regular file 'thesis_backup/quotations.txt'? y
The -i option will prompt before (every) removal (use Y to confirm deletion or N to keep the file). The Unix shell doesn’t have a trash bin, so all the files removed will disappear forever. By using the -i option, we have the chance to check that we are deleting only the files that we want to remove.

If we try to remove the thesis directory using rm thesis, we get an error message:

$ rm thesis

rm: cannot remove `thesis': Is a directory

This happens because rm by default only works on files, not directories.

rm can remove a directory and all its contents if we use the recursive option -r, and it will do so without any confirmation prompts:

$ rm -r thesis

Given that there is no way to retrieve files deleted using the shell, rm -r should be used with great caution (you might consider adding the interactive option rm -r -i).

Operations with multiple files and directories

Oftentimes one needs to copy or move several files at once. This can be done by providing a list of individual filenames, or specifying a naming pattern using wildcards.

Copy with Multiple Filenames

For this exercise, you can test the commands in the data-shell/data directory.

In the example below, what does cp do when given several filenames and a directory name?
$ mkdir backup
$ cp amino-acids.txt animals.txt backup/
In the example below, what does cp do when given three or more file names?
$ ls -F
amino-acids.txt  animals.txt  backup/  elements/  morse.txt  pdb/  planets.txt  salmon.txt  sunspot.txt
$ cp amino-acids.txt animals.txt morse.txt
Solution

If given more than one file name followed by a directory name (i.e. the destination directory must be the last argument), cp copies the files to the named directory.

If given three file names, cp throws an error such as the one below, because it is expecting a directory name as the last argument.
cp: target ‘morse.txt’ is not a directory

Using wildcards for accessing multiple files at once

Wildcards

* is a wildcard, which matches zero or more characters. Let’s consider the data-shell/molecules directory: *.pdb matches ethane.pdb, propane.pdb, and every file that ends with ‘.pdb’. On the other hand, p*.pdb only matches pentane.pdb and propane.pdb, because the ‘p’ at the front only matches filenames that begin with the letter ‘p’.

? is also a wildcard, but it matches exactly one character. So ?ethane.pdb would match methane.pdb whereas *ethane.pdb matches both ethane.pdb, and methane.pdb.

Wildcards can be used in combination with each other e.g. ???ane.pdb matches three characters followed by ane.pdb, giving cubane.pdb ethane.pdb octane.pdb.

When the shell sees a wildcard, it expands the wildcard to create a list of matching filenames before running the command that was asked for. As an exception, if a wildcard expression does not match any file, Bash will pass the expression as an argument to the command as it is. For example typing ls *.pdf in the molecules directory (which contains only files with names ending with .pdb) results in an error message that there is no file called *.pdf. However, generally commands like wc and ls see the lists of file names matching these expressions, but not the wildcards themselves. It is the shell, not the other programs, that deals with expanding wildcards.

List filenames matching a pattern

When run in the molecules directory, which ls command(s) will produce this output?

ethane.pdb methane.pdb

ls *t*ane.pdb

ls *t?ne.*

ls *t??ne.pdb

ls ethane.*

Solution

The solution is 3.

1. shows all files whose names contain zero or more characters (*) followed by the letter t, then zero or more characters (*) followed by ane.pdb. This gives ethane.pdb methane.pdb octane.pdb pentane.pdb.

2. shows all files whose names start with zero or more characters (*) followed by the letter t, then a single character (?), then ne. followed by zero or more characters (*). This will give us octane.pdb and pentane.pdb but doesn’t match anything which ends in thane.pdb.

3. fixes the problems of option 2 by matching two characters (??) between t and ne. This is the solution.

4. only shows files starting with ethane..

More on Wildcards

Sam has a directory containing calibration data, datasets, and descriptions of the datasets:

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│   ├── calibration
│   └── datasets
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    └── all_november_files

Before heading off to another field trip, she wants to back up her data and send some datasets to her colleague Bob. Sam uses the following commands to get the job done:

$ cp *dataset* backup/datasets
$ cp ____calibration____ backup/calibration
$ cp 2015-____-____ send_to_bob/all_november_files/
$ cp ____ send_to_bob/all_datasets_created_on_a_23rd/

Help Sam by filling in the blanks.

The resulting directory structure should look like this

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│   ├── calibration
│   │   ├── 2015-10-23-calibration.txt
│   │   ├── 2015-10-26-calibration.txt
│   │   └── 2015-11-23-calibration.txt
│   └── datasets
│       ├── 2015-10-23-dataset1.txt
│       ├── 2015-10-23-dataset2.txt
│       ├── 2015-10-23-dataset_overview.txt
│       ├── 2015-10-26-dataset1.txt
│       ├── 2015-10-26-dataset2.txt
│       ├── 2015-10-26-dataset_overview.txt
│       ├── 2015-11-23-dataset1.txt
│       ├── 2015-11-23-dataset2.txt
│       └── 2015-11-23-dataset_overview.txt
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    │   ├── 2015-10-23-dataset1.txt
    │   ├── 2015-10-23-dataset2.txt
    │   ├── 2015-10-23-dataset_overview.txt
    │   ├── 2015-11-23-dataset1.txt
    │   ├── 2015-11-23-dataset2.txt
    │   └── 2015-11-23-dataset_overview.txt
    └── all_november_files
        ├── 2015-11-23-calibration.txt
        ├── 2015-11-23-dataset1.txt
        ├── 2015-11-23-dataset2.txt
        └── 2015-11-23-dataset_overview.txt

Solution

$ cp *calibration.txt backup/calibration
$ cp 2015-11-* send_to_bob/all_november_files/
$ cp *-23-dataset* send_to_bob/all_datasets_created_on_a_23rd/

Organizing Directories and Files

Jamie is working on a project and she sees that her files aren’t very well organized:
$ ls -F
analyzed/  fructose.dat    raw/   sucrose.dat
The fructose.dat and sucrose.dat files contain output from her data analysis. What command(s) covered in this lesson does she need to run so that the commands below will produce the output shown?
$ ls -F
analyzed/   raw/
$ ls analyzed
fructose.dat    sucrose.dat
Solution
mv *.dat analyzed
Jamie needs to move her files fructose.dat and sucrose.dat to the analyzed directory. The shell will expand *.dat to match all .dat files in the current directory. The mv command then moves the list of .dat files to the ‘analyzed’ directory.

Reproduce a folder structure

You’re starting a new experiment, and would like to duplicate the directory structure from your previous experiment so you can add new data.

Assume that the previous experiment is in a folder called ‘2016-05-18’, which contains a data folder that in turn contains folders named raw and processed that contain data files. The goal is to copy the folder structure of the 2016-05-18-data folder into a folder called 2016-05-20 so that your final directory structure looks like this:
2016-05-20/
└── data
    ├── processed
    └── raw
Which of the following set of commands would achieve this objective? What would the other commands do?
$ mkdir 2016-05-20
$ mkdir 2016-05-20/data
$ mkdir 2016-05-20/data/processed
$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ cd data
$ mkdir raw processed
$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20/data/processed
$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ mkdir raw processed
Solution

The first two sets of commands achieve this objective. The first set uses relative paths to create the top level directory before the subdirectories.

The third set of commands will give an error because mkdir won’t create a subdirectory of a non-existant directory: the intermediate level folders must be created first.

The final set of commands generates the ‘raw’ and ‘processed’ directories at the same level as the ‘data’ directory.

Key Points

cp old new copies a file.

mkdir path creates a new directory.

mv old new moves (renames) a file or directory.

rm path removes (deletes) a file.

* matches zero or more characters in a filename, so *.txt matches all files ending in .txt.

? matches any single character in a filename, so ?.txt matches a.txt but not any.txt.

Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.

The shell does not have a trash bin: once something is deleted, it’s really gone.

Most files’ names are something.extension. The extension isn’t required, and doesn’t guarantee anything, but is normally used to indicate the type of data in the file.

Depending on the type of work you do, you may need a more powerful text editor than Nano.

Intro to COLA Computing

Logging into COLA Computers

Overview

Why do I need to login to another computer instead of using my own computer?

COLA Computers

Setting up Software for your computer

macOS

Windows

Linux

Download and install the correct ssh software for your computer

In this class, you can

Logging in

On macOS

On Windows

Password Requirements & Policies

Login to a different COLA computer

Key Points

Shell Commands

Overview

Background

The Shell

Exploring More ls Flags

Solution

Listing in Reverse Chronological Order

Solution

Getting help

Key Points

Navigating Files and Directories

Overview

Moving around files and directories

Two More Shortcuts

Absolute vs Relative Paths

Solution

Key Points

Working With Files and Directories

Overview

Creating directories

Step one: see where we are and what we already have

Create a directory

Good names for files and directories

Creating A File

Solution

Moving files and directories

Moving Files to a new folder

Solution

Copying files and directories

Renaming Files

Solution

Moving and Copying

Solution

Removing files and directories

Deleting Is Forever

Using rm Safely

Solution

Operations with multiple files and directories

Copy with Multiple Filenames

Solution

Using wildcards for accessing multiple files at once

Wildcards

List filenames matching a pattern

Solution

More on Wildcards

Solution

Organizing Directories and Files

Solution

Reproduce a folder structure

Solution

Key Points

Exploring More `ls` Flags

Using `rm` Safely