Setting up your working environment

Background information: UNIX and basic command to use (a brief review):

Note: please change the default cluster name if necessary

prd.vital-it.ch (UNIL)
frt.el.vital-it.ch (EPFL)
frt.ug.vital.it.ch (UNIGE)


UNIX documentation (background info in case you need help with UNIX): http://edu.isb-sib.ch/course/view.php?id=82

  • Simple text editor: nano
  • To copy files from local machine to prd.vital-it.ch:
    • scp filename username@prd.vital-it.ch
    • Copy program on Windows: http://winscp.net
    • Copy program on Max OS X: http://rsug.itd.umich.edu/software/fugu/
Hint: you can also directly copy the example files to your current folder on prd.vital-it.ch with the following command:

wget ftp://ftp.vital-it.ch/edu/HPC/examples-files.tar.gz


Important:

    • We recommend that you create a folder in /scratch/cluster/daily/ and that you perform all the exercises there. At the end of the workshop, you can copy the files you want to keep on your local machine.

Do not forget to replace <username> in the following examples with your actual username!

1) login to cluster front-end
Using a command line terminal (UNIX shell or putty on Windows), log in to the Vital-IT (UNIL) cluster front-end machine:

ssh <username>@prd.vital-it.ch
pwd

2) Create a directory in /scratch/daily/

cd /scratch/cluster/daily/
mkdir <username>
cd <username>

3) Download a copy of the example files to your current folder

wget ftp://ftp.vital-it.ch/edu/HPC/examples-files.tar.gz
tar -ztvf examples-files.tar.gz
(the 't' lists the content of the archive. Notice the dates of the files.)
tar -zxvmf examples-files.tar.gz
(the 'm' preceeding the f - for 'modification-time' will set the current date and time to the files. Why could this be important?)
cp /db/HPC-course/ga/hpc-ga-ex-scripts.tar.gz .
tar -zxvmf hpc-ga-ex-scripts.tar.gz

4) Cleaning up and preparing for the exercises

rm examples-files.tar.gz
mkdir exercise_blast
mv examples-files/*blast* exercise
_blast/
mv examples-files/p123456.seq exercise_blast/
rm hpc-ga-ex-scripts.tar.gz
mkdir exercise_ga
mv *.sh soap.config exercise_ga

5) Additional file

On your laptop:
- go to: "http://www.ebi.ac.uk/ena/data/view/AF311055&display=fasta"
- save the file as 'AF311055' on your laptop.
- Copy the 'AF311055' file on Vital-IT:

a) using winscp or fugu
or
b) using the terminal
scp AF311055 <username>@prd.vital-it.ch:/scratch/cluster/daily/<username>/exercise_blast/
- On Vital-IT server, in the exercise_blast/ directory, rename the 'AF311055' file to 'thio_rat.dna'
mv AF311055 thio_rat.dna


6) UNIX permissions

Go in the examples-files directory and try to execute the shell script simple-without-exec-permission.sh
using the following command (including ./ !):
./simple-without-exec-permission.sh

What is wrong ?
Hints: look at the file permissions or ... man chmod

Last modified: Thursday, 21 April 2016, 12:18 PM