Preliminaries: Using the commandline, signing into a server, and submitting jobs to a HPC

How to sign into a server

1. The first thing you will need is a terminal application

A. Mac users, you have this already (Terminal). Finder > Terminal

B. Windows users, you have several options. I prefer MobaXterm, PuTTy, or GitBash.

PuTTy

MobaXterm -- has a nice little window built in!

GitBash

2. File transfer drag/drop applications:

FileZilla -- for any platform

WinSCP -- a nice application for Windows users

3. Text editors

bbedit -- for mac users. You may already have this with you OS distribution.

Notepad++ -- no, not the native "notepad" application!

4. OK, now you have your terminal application open. Now what? you should see the following:

[cfb0001.LSB5218] >

### or something like that...

Let's log into a server:

### General usage below. You will use YOUR username, my server address, etc.
ssh username@servername.server.address.edu

### Now, enter your case-sensitive password.
### Once you have successfully logged in, to may need to type:
bash

### This will enter you into the bash shell (before you might have just been in the Linux system but not in bash)
### to log off, type 'exit'

Logging into ‘myco’ (the Barrett Lab server) and a HPC cluster: this is a short video by Dhanu Ramachandran, our CPING postdoc.

Now, try out the following commands:

man
man ls
man grep
clear
history
date
whoami
id
groups
who
last
hostname
w
uname
ls
ls -l
ls -a
touch file1.txt
ls
cp file1.txt file2.txt
ls
mv file2.txt file3.txt
ls   # to see what just happened -- how does it compare to 'cp'?
head file1.txt # this is a blank file!
echo "How's it going?" >> file1.txt
head file1.txt
cat file1.txt
echo "ATGGTGACGTGCAAACGTGTGTGTGTGTGTGTG" > file2.txt
head file2.txt
cat file1.txt file2.txt > file3.txt ; head file3.txt
less file3.txt    # press 'q' to quit
top   # list all current processes. This allows you to check who is running what. press 'q' to exit.
htop  # A super fancy version of top. Use this to monitor RAM usage across multiple cores on a server. Press 'F10' button to exit
# kill ### DON'T enter this now, but this is how you stop a particular process
ln   #make links between files
pwd
cd ..
ls
pwd
cd -
pwd
mkdir new_directory
ls new_directory

5. Some important places in the directory structure

pwd             # where am I?
cd ~            # go to home folder
cd /            # go to the ROOT of the directory structure
cd /home/cbarrett     # The absolute path to your home folder. This always leads with the ROOT '/'
cd /usr/local/src     # We typically use this folder to store source code before compiling new software. Download new software here
cd /usr/local/bin     # This is where we keep our binaries, the compiled, executable software
cd /data              # This is where we store everyones' data
cd /data/cbarrett     # This is where I store my data
cd /data/cbarrett [press tab twice]   # This will list all the subdirs of /data/cbarrett

6. SUDO -- this is a really important thing to do in linux, e.g. Ubuntu linux.

sudo                   # To see some options
sudo [some_command]    # Enter your login password. This will give you permission to do things like modify files and run software                                                        # It is really just a security thing, giving you elevated permissions to run admin tasks

Some more information on sudo

7. Submitting jobs to a High Performance Computing cluster

Dhanu's GitHub site: HPC job submission

8. Setting up your $PATH: Telling UNIX where to find installed software

Two choices:

A. Simply copy & paste the code below

export PATH=/usr/local/bin:$PATH
export PATH=/usr/bin:$PATH
export PATH=/usr/local/src:$PATH
export PATH=/usr/local/src/ncbi-blast-2.10.1+/bin:$PATH
export PATH=/data/mmckain/Fast-Plast:$PATH
source ~/.bashrc

B. Edit your .bashrc file and paste in the text below, then save

sudo nano ~/.bashrc         
### This is your bashrc profile, which tells UNIX where to look for software

export PATH=/usr/local/bin:$PATH
export PATH=/usr/bin:$PATH
export PATH=/usr/local/src:$PATH
export PATH=/usr/local/src/ncbi-blast-2.10.1+/bin:$PATH
export PATH=/data/mmckain/Fast-Plast:$PATH

Then type:

source ~/.bashrc

Save and exit:

ctrl+X
### To save and exit