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Description Hands On Lab Exercises for HPC
Related-course materials HPC
Authors Ndomassi TANDO (
Creation Date 14/03/2018
Last Modified Date 20/03/2019



Getting connected to a Linux servers from Windows with SSH (Secure Shell) protocol
Platform Software Description url
mobaXterm an enhanced terminal for Windows with an X11 server and a tabbed SSH client more
putty Putty allows to connect to a Linux server from a Windows workstation. Download
Transferring and copying files from your computer to a Linux servers with SFTP (SSH File Transfer Protocol) protocol
Platform Software Description url
filezilla FTP and SFTP client Download
Viewing and editing files on your computer before transferring on the linux server or directly on the distant server
Type Software url
Distant, consol mode nano Tutorial
Distant, consol mode vi Tutorial
Distant, graphic mode komodo edit Download
Linux & windows based editor Notepad++ Download

Practice 1: Get Connecting on a linux server by ssh

In mobaXterm:

  1. Click the session button, then click SSH.
    • In the remote host text box, type:
    • Check the specify username box and enter your user name
  2. In the console, enter the password when prompted. Once you are successfully logged in, you will be use this console for the rest of the lecture.
  3. Type the command qhost and comment the result
  4. type the command qhost -q and noticed what have been added

Practice 2: Reserve one core of a node using qrsh and create your working folder

  1. Type the command qstat and noticed the result
  2. Type the command qstat -u "*"and noticed the difference
  3. Type the command qrsh -q formation.q then qstatagain
  4. Type the command qstat and noticed what have been added
  5. Create your own working folder in the /scratch of your node:
cd /scratch
 mkdir formationX
  1. Type the following command with the nodeX of your choice expect the one you are already connected to
ssh nodeX "ls -al /scratch/"

Tip: you can use qlogin instead of qrsh if you want to use graphical software

Practice 3 : Transferring files with filezilla sftp

Download and install FileZilla
Open FileZilla and save the IRD cluster into the site manager

In the FileZilla menu, go to File > Site Manager. Then go through these 5 steps:

  1. Click New Site.
  2. Add a custom name for this site.
  3. Add the hostname to have access to /data2/formation
  4. Set the Logon Type to “Normal” and insert your username and password used to connect on the IRD cluster
  5. Press the “Connect” button.
Transferring files

  1. From your computer to the cluster : click and drag an text file item from the left local colum to the right remote column
  2. From the cluster to your computer : click and drag an text file item from he right remote column to the left local column
  3. Retrieve the file HPC_french.pdf from the right window into the folder /data/projects/formation/

Practice 4: Transfer your data from the nas server to the node

  1. Using scp, transfer the folder TPassembly located in /data2/formation into your working directory
  2. Check your result with ls

Practice 5: Use module environment to load your tools

  1. Load ea-utils V2.7 module
  2. Check if the tool are loaded

Practice 6 : Launch analyses

Get stats on fastq

  1. Go into the folder TPassembly/Ebola
  2. Launch the command fastq-stats ebola1.fastq
  3. Launch the command fastq-stats -D ebola1.fastq

Perform an assembly with abyss-pe

With abyss software, we reassembly the sequences using the 2 fastq files ebola1.fastq and ebola2.fastq

Launch the commands

module load bioinfo/abyss/1.9.0
qsub -q formation.q -l hostname=nodeX -cwd -b y abyss-pe k=35 in=\'ebola1.fastq ebola2.fastq\' name=k35

Practice 7: Transfering data to the nas server

  1. Using scp, transfer your results from your /scratch/formationX to your /home/login
  2. Check if the transfer is OK with ls

Practice 8: Deleting your temporary folder

 cd /scratch
rm -r formationX

Practice 9: Launch a job with qsub

Following the several steps performed during the practice, create a script to launch the analyses made in practice6:

1er step: create the SGE section in your script

1) Set a name for your job

2) Precise your email

3) Choose the bioinfo.q queue

2nd step: type the commands you want the script to launch:

1) create a personal folder in /scratch with mkdir

2) Using scp, transfer the folder TPassembly located in /data2/formation into your working directory

3) Launch abyss version 1.9.0 with module load

4) Into the the folder TPassembly/Ebola, lanch the following command:

abyss-pe k=35 in='ebola1.fastq ebola2.fastq' name=k35

5) Using scp, transfer your results from your /scratch/formationX to your /home/login

6) Delete the personal folder in the /scratch


We are going to launch a 4 steps analysis:

1) Perform a multiple alignment with the nucmer tool

2) Filter these alignments with the delta-filter tool

3) Generate a tab file easy to parse the with show-coords tools

4) Generate a png image with mummerplot

 qsub -q formation.q
qacct -j JOB_ID
ssh nodeX rm -rf /scratch/formationX


The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).