Command Line Basics

Logging in

Start up Terminal (or PuTTY), if you have an RCDS account:


If not, an account will have been created for you on our classroom servers:


other options

You should see our Message Of The Day (MOTD)

Benjamins-iMac:chef-cookbooks boswald$ ssh's password:

   WARNING: To protect the system from unauthorized use and to
   ensure that the system is functioning properly, activities
   on this system are monitored recorded and subject to audit.
   Use of this system is expressed consent to such monitoring
   and recording. Any unauthorized access or use of this system
   is prohibited and subject to criminal and civil penalties.

   |        Current Standalone System Usage        |
   |          SERVER   MEM Usage(%)   CPU Usage(%) |
   |           colin           2.48           0.00 |
   |            ford           3.27           0.29 |
   |          marvin           5.87           6.22 |
   |          slarti           7.68           0.64 |
   |          hactar          24.15           0.68 |
   |        trillian           4.00           0.07 |
   |          arthur           1.29           2.00 |
   |           whale           1.53           1.70 |
   |          zaphod          29.41           0.11 |

   CORES:   16
   MEMORY:  60445 MB
   SUMMARY: (collected Thu Sep  8 16:05:01 PDT 2016)
      * CPU Usage (total average) = 6.41%
      * Memory used (real)        = 14010 MB
      * Memory free (cache)       = 56634 MB
      * Swap in use               = 872 MB
      * Load average              = 1.00  1.00  1.00

   QUESTIONS: Submit all questions, requests, and system issues

  Good afternoon Benjamin

benji@marvin ~ $

Note the server name you just logged into in the usage table. If it’s especially busy (CPU Usage > 70%), you’ll be better off logging into a different server.

Your Home Directory

When you log in you are brought to your home directory by default


Should get the response


No matter which server you log into, your home directory will be the same. This is the magic of distributed file systems.


By default you are running in the Bash Shell, which is how you interact with the file system, start programs etc. If you want to search for a command, include the word bash in your query. For example you could google ‘bash create directory path’. Here are some of the most common and useful bash commands:

  • ls - show me the contents of the current directory

  • mkdir <dir_name> - create a new directory

    mkdir your_name_here

  • cd <dir_name> - change directory

    cd your_name_here

  • cd .. - change to the parent directory


benji@marvin ~ $ mkdir workshop
benji@marvin ~ $ cd workshop
benji@marvin ~/workshop $ cd ..
  • nano <filename> - edit (and create if necessary) a file

    nano somefile.txt

  • rm <filename> - delete a file

  • mv <filename> <destination> - move or rename a file

  • man <command> - show help documentation

  • which <command> - locate the actual executable file of a command (and test whether it exists)
  • top - show system utilization

  • cat <filename> - print the contents of a file to screen (std out)

  • less <filename> - show the contents of a file interactively

Getting data to the server

To download data directly from the internet, use wget

Lets get some data to work with, Mycobacterium tuberculosis 16S Ribosomal RNA

wget -nc

If your data is on your local computer, you can scp the data to the server:

scp /path/to/local/data

*Note: SCP does not deal well with spaces in paths or filenames.

Other options:

Using the RCDS’s installed software

We use the environment modules package to dynamically load/unload most all of the specialized software.

module avail

To load a module use:

module load module_name/[version]

For example:

module load clustalw

And run:

clustalw2 Myco.tb.fasta -output=nexus

Now that we’ve aligned the sequences - let’s make a tree using MrBayes. First create a MrBayes command file with nano that contains:

begin mrbayes;
   set autoclose=yes nowarn=yes;
   execute Myco.tb.nxs;
   lset nst=6 rates=gamma;
   mcmc nruns=1 ngen=10000 samplefreq=10 file=Myco.tb.mbout1;
   sumt burnin=500;

Load the MrBayes module and run that file

module load mrbayes

MrBayes chokes on our nexus file because it doesn’t like ‘|’ characters in the species names. So let’s use some command line voodoo to change those things.

head -n 25 Myco.tb.nxs
head -n 25 Myco.tb.nxs | sed -r "s/gi\|.*gb\|(.*)\.1\|(.*)/\1\2/g"

Sed You’ll probably need to spend some time with the regular expressions to make it work. Once it’s tuned - perform the actual substitution, and edit our file from above to use the new file

cat Myco.tb.nxs | sed -r "s/gi\|.*gb\|(.*)\.1\|(.*)/\1\2/g" > Myco.tb.mb.nxs

The | character is commonly called a pipe, which takes the output from one command and dumps it to the next. The cat command by default prints to STDOUT (the screen), but we ‘piped’ it to sed which is a character stream editor (Sed tutorial). The command sed also by default prints to STDOUT, but we directed the output to a file with the > command. The > command creates or overwrites whatever file name follows it - without warning! - so you need to be careful using it. To append to the end of a file, use the >> command.

Try the mrbayes run again


It works!

Another useful command is grep, which is mostly used for searching through files. For example we could effectivly pull out the sequence data for one of the species in our alignment file with:

grep "AF498004" Myco.tb.mb.nxs

benji@marvin ~/workshop $ grep "AF498004" Myco.tb.mb.nxs
AF498004   --------------------------------------------------
AF498004   --------------------------------------------------
AF498004   AGGGTTTC-CAAAGGNNNTNAAA---------------------------
AF498004   --------------------------------------------------
AF498004   --------------------------------------------------
AF498004   -----------------------------------------------

We’re starting to generate a bunch of files, so let’s clean up. First make a new directory and then move files into it using the glob or * character.

mkdir Myco
mv Myco.tb.* Myco/

The * character is a wildcard - it will match any character(s). Now let create a single compressed archive of all the Myco.tb files.

tar -cjf Myco.tar.bz2 Myco

The tar (tape archive) command used with the -c option creates an archive (single file) from a directory or a list of files. The -j option specifies that we want the archive compressed to save disk space, and the -f option is for specifying the archive file name. Note that tar does not remove the original files, you have to explicitly do that:

rm -rf Myco

The archive file is now easy to retrieve using scp. Let’s un-archive those files and work with them some more:

tar -xf Myco.tar.bz2
cd Myco


If you were really wanting to create a good phylogeny for these Mycobacterium, you would want to run MrBayes for much longer. However, you also don’t want to have to stay logged into the RCDS servers while the program is running. In order to keep a program running without being logged in, use the screen command.


What happened? You’re now running commands inside a new interactive shell that you can detach from by pressing Ctrl-A then Ctrl-D. Lets start a longer running MrBayes job. Edit your file so that the number of generations is 200000. And then start it.


Now detach from the screen with Ctrl-A then Ctrl-D

benji@marvin ~/workshop/Myco $ screen
benji@marvin ~/workshop/Myco $

And you should be able to see your MrBayes still running by using the top (or htop)command:

top -u benji

At this point you could log out, and MrBayes would continue on until it finished. You reattach with:

screen -r

When you’re done with a screen, close it out by typing exit when you’re in the screen.

Now is as good a time as any to say - be a good computational neighbor. Our servers are shared by many researchers, so please don’t start a computationally intensive job on a server that is already really busy (pay attention to the MOTD, or use top/htop). The servers will cope relatively well with an overloaded processor, but if you run them out of memory - first they slow down markedly as they start to use hard disk space to offload memory (called swapping). Then the system basically goes crazy and starts a process called OOM killer, which pretty much randomly kills things in a last ditch effort to keep the system from becoming completely frozen.

If you accidentally start a process running and want to stop it use Ctrl-C (when it’s running interactively). If you know the process id (from top) you can stop it with the kill command.

kill 2345

Command History

If you use the up and down arrow keys, you can scroll through all the commands you’ve previously entered. To see a list of all the commands you’ve entered, use the history command. When you have a bunch of commands in you history (it will store about 1000), pipe the history through another command like less or tail.

history | less
history | tail -n 40

Programming in Bash

You can write a program to do whatever you want using only Bash - but the syntax is a bit different than most other programming languages. First and foremost, spaces matter. In most programming languages the following three lines are equivalent:

a = 10
a= 10

In Bash, only the first is correct. Once you assign a value to a variable, refer to it by prepending a $

echo $a

The echo command simple means print to the screen (STDOUT). If you just enter $a, the Bash shell will try to run the command 10 (and give you an error). Similarly, only the first of these commands will work:

if [ $a -lt 11 ]; then echo "less than eleven"; fi
if[ $a -lt 11]; then echo "less than eleven"; fi
if [$a -lt 11]; then echo "less than eleven"; fi

Let’s experiment with looping and conditionals. First, let’s create a new directory

cd ..
mkdir bashfun
cd bashfun

Now let’s create a bunch of input files from the built in $RANDOM variable

for i in {1..50}; do echo $RANDOM > num.$i; done

As an exercise, we’ll now create two directories and sort the file by whether the numbers in them are even or odd.

mkdir even odd
for nf in $(ls num.*); do rn=$(cat $nf); if [ $(expr $rn % 2) -eq 0 ]; then mv $nf even/ ; else mv $nf odd; fi ; done
ls even
ls odd
cat even/*
cat odd/*

Let’s deconstruct the above for statement:

                       # when you wrap text in a $(), that tells Bash to execute the commands within
for nf in $(ls num.*)  # list all the files that start with num. and loop over them 
 do                    # starts the execution loop
   rn=$(cat $nf)       # read the file with the name stored in nf and store it as rn
                       # this really only works when the file contains a single line
   if [ $(expr $rn % 2) -eq 0 ] # expr tells Bash to do mathematical operations
     then                       # % means modulo, or the remaider of integer division
                                # compare numbers in Bash with -lt -gt and -eq
      mv $nf even/     # move the file to the even directory
   else                # the above if returned false, so
      mv $nf odd;      # move the file to the odd directory
   fi                  # end if command
done                   # end for loop


All of the above commands could be put into a script, and then executed repeatedly. Here’s what that would look like:


# create a bunch of random numbers
for i in {1..50}; do echo $RANDOM > num.$i; done

# sort them
for nf in $(ls num.*); do 
  rn=$(cat $nf) 
  if [ $(expr $rn % 2) -eq 0 ]; then 
    mv $nf even/
    else mv $nf odd

Create a file named with the above script. The first line is called the shebang line, and indicates what interpreter to use to run the script - in our case Bash (other options could be python or perl etc…). Comment lines start with a #, and are skipped over by Bash. To make this script executable, we need to set the executable bit

chmod +x

Then we can execute it with:


Why the ./? This tells Bash to look in the current directory for the executable, which it would otherwise not do - because it is a security risk. Bash looks for executables in the $PATH. To see what directories are currently in the $PATH, we can just echo it out.

echo $PATH

If you’ve still got the modules from above loaded, you should see their direcotories listed. Unload the modules and see how the $PATH changes.

module unload mrbayes
echo $PATH

Mostly, the module command just manipulates your $PATH (It also can set other environment variables and load other modules).

Let’s modify our script to accept a command line argument - the number of random number files to generate.


if [ -z $1 ]; then
  echo "You need to enter a number"
# create a bunch of random numbers
for i in $(seq 1 $1); do echo $RANDOM > num.$i; done

# sort them
for nf in $(ls num.*); do 
  rn=$(cat $nf) 
  if [ $(expr $rn % 2) -eq 0 ]; then 
    mv $nf even/
    else mv $nf odd

Command line arguments are passed to a script in the variables $1, $2, $3 … etc. (the variable $0 contains the name of the script/command). At the top of the script we check to see if the $1 variable is empty (-z), and if it is the script exits. Now if we run our script with a number, it will generate that many files.

./ 10

Of course, there are more advanced methods to parse command line arguments.

Practice exercises:

  • modify the script to print out the mean of the evens and the mean of the odds
  • modify the script to create two files - one of the even numbers and one of the odd numbers, and sort the numbers in each file