Start by entering

pwd

This will print your present working directory (the directory you are currently in). You will probably see this:

/home/moleuser

indicating that you are in your home directory.

Next, type:

ls

This lists the contents of your working directory (which is currently empty unless you have created some files already).

You can also look at the contents of any other directory by supplying the path. For instance,

ls /usr/local/share/examples/mole

will list the contents of the directory in which most of the example data files we will be using are stored.

To create a new folder (directory) inside your present working directory, type

mkdir myfolder

Type ls and then enter. Your newly created folder should be listed.

We can also use the ls command with flags at this point. Typing

ls -l

will list the contents of the current directory in long format which includes information about permissions and file size.

ls -ltr

will list the contents of the current directory in long format, and in time (t) reversed (r) order. This makes it easy to see what files are newest.

You can move into the new folder you made by typing

cd myfolder

You can use pwd to confirm you’ve moved and are now in a new working directory. You can move back to your home directory by typing cd with no arguments. This is a handy trick if you are lost in the filesystem and want to get home!

cd

Confirm you are in your home directory using pwd.

Copying, renaming, and moving files

Move into the myfolder directory that you just created:

cd ~/myfolder

Create a file called tmp1.txt in the nano editor and put whatever you want inside of it:

nano tmp1.txt

After typing something, use Ctrl-X to exit (hold down the control key and type x). Type ‘Y’ and enter to save your changes.

Use the head command to look at the beginning of the file you created:

head tmp1.txt

The concatenated (cat) command can be used to spit out the entire file (when head does not show enough of the file). The cat command can be used to concatenate several files, but if you give it just one file it will show you the contents of the file:

cat tmp1.txt

The copy command (cp) is used to copy files to new places. Make a copy of tmp1.txt called tmp2.txt by typing:

cp tmp1.txt tmp2.txt

We can also cp a file from the shared directory using absolute and relative paths:

cp /usr/local/share/examples/mole/MSAlab/example.tre .

will copy the file named example.tre to your current directory but will not change its name. Use ls to verify that your myfolder directory now contains the file example.tre.

The move command (mv) can be used to move or rename files. Try renaming tmp2.txt to example.txt:

mv tmp2.txt example.txt

You can move the example.txt file to your home folder using mv as well:

mv example.txt ..

The above command moves the example.txt file to the parent directory of your current directory. Use

ls ..

to check that it is in the parent directory.

NOTE: Do not move files that are not in your home directory or a subdirectory thereof. All files in shared or root folders are to be copied, never moved.

Downloading files from the internet

In order to get a file from an online source you can use the curl command. Type:

curl -O <url>

Where the <url> stands for the web address of the file you wish to download. For example

curl -O https://molevolworkshop.github.io/assets/data/yule.tre

This will download the file yule.tre to your present working directory. The -O flag is important: it tells curl that you wish to save the file under the same name as on the remote web site. Without specifying -O, curl will simply spill out the file contents to the console, which is not what you want in most cases.

For more info on using the linux shell check out the Software Carpentry tutorial

Creating an alias for the example data directory

You can create an alias (known as a symbolic link, or symlink for short) to a directory to save a lot of future typing. Start by typing

cd

to return to your home directory. Now type the following command to create a symbolic link named eg that points to the directory /usr/local/share/examples/mole:

ln -s /usr/local/share/examples/mole eg

Use the ls command to confirm that the symlink was indeed created:

ls -l

Note that the long format shows the directory to which a symlink points. You can now show the contents of the /usr/local/share/examples/mole directory with very little typing:

ls eg

Tips for making things easier

  • Use the up arrow to see commands you have typed previously. This can save a lot of typing

  • Type history to see a list of all your old commands. If you see the one you want, you can run it again using an exclamation point followed by the command number. For example, !24 would re-execute command number 24.

  • You can type Ctrl-R to search for a command you typed previously. Just start typing and, when you see the command you want, press enter to run it.

  • If you use cd to navigate to a new directory, typing ```cd -`` takes you back to the previous directory.