5. Work in remote computer

1. Login to your ibex account

2. Enter your password (email/portal passwd)

3. View current directory

4. Copy your local folder to your remote directory.

scp -r folderpath username@ipaddress:path_to_copy

5. There are many bio packages already installed in ibex. Search those with module avail. If you find it, load it with module load package_name. If not, you can load anaconda and set your own environment, install the packages you want !

6. You should never perform a job in head node. You rather submit the job to available nodes. Use Slurm scripts, which are nothing but a language to communicate with clusters. You can generate one slurm script using ibex jobscript generator

Ibex jobscript generator

7. Copy that to a text file, add the one-liner from previous section (3. Batch operations, step 1, line no.5) and save it as .sh file.

scp slurmscript1.sh username@address:path_to_copy. Notice that -r is to copy entire directory

IMPORTANT: Add -P after grep. i.e. grep -P "\tgene".... In linux you have to explicitly tell to use Perl type regex.

8. Submit it with sbatch slurmscript1.sh

9. View the job status with squeue -u username

10. You will receive email at beginning of the job and at the end of the job !

Summary:

Now you know to login to remote computer (RC) --> copy file from local computer to remote computer --> check for installed module in RC --> Load the module --> create a slurm file --> submit a job --> check the status of job --> look at the output generated !