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/
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
3) 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
4) 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- On Vital-IT server, in the exercise_blast/ directory, rename the 'AF311055' file to 'thio_rat.dna'
or
b) using the terminal
scp AF311055 <username>@prd.vital-it.ch:/scratch/cluster/daily/<username>/exercise_blast/
mv AF311055 thio_rat.dna
5) 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.shHints: look at the file permissions or ... man chmod
What is wrong ?