Biows

General requirements

Get a 64-bit workstation that has multiple cores (4 is best) and lots of RAM (32 Gb). Also lots of storage will be required - large HDD (or several) is a must.

Install one of the LTS (long-term stable) versions of Ubuntu.

Do's and dont's

List of necessary programs: general purpose bioinformatics

• Java
• samtools
• bedtools
• UCSC tools
• IGV and igvtools
• R (and packages within)
• FastQC
• GENE-E

Remote access and operations

In order to be effective working on the remote Unix computer, you need to master two things:

• Bash scripting
• Using a text-only text editor

Using aliases

In order to speed up routine processes, such as logging into a remote computer, or changing into a directory with a long name, use aliases.

To do this, go to your home directory, and find hidden file .bashrc.

After opening it with your favourite text editor, add lines like these:

alias 769='ssh apredeus@unit-769.times.labs.intellij.net'
alias 770='ssh apredeus@unit-770.times.labs.intellij.net'
alias cd1='cd /media/DISK1/reference'
alias cd2='cd /media/DISK2/My_very_difficult_project'

This will allow you to simply type "769" next time you want to log in to workstation unit-769 (You have to re-load your Bash to see the effect).

Using passwordless SSH

This also saves a lot of time when SSH-ing from your workstation (WS1) onto another one (WS2). Just follow these steps:

1. On WS1, go to your home directory. Run ls -alt to see if you have a directory named .ssh. If not, create it. After this, run

ssh-keygen -t rsa -b 4096

Just press "Enter" for all questions. After this, do

cat ~/.ssh/id_rsa.pub

and copy the result into buffer.

2. In a separate terminal, log into WS2 using your password and go to your home directory. Run ls -alt to see if you have a directory named .ssh. If not, create it.

After this, open the file ~/.ssh/authorized_keys for editing (with any text editor), and paste the key you generated and copied into the buffer in pt.1

Save the changes.

3. Try logging in again. You should be good to go.

If all the files are in order and it still does not work, check the permissions on the .ssh folder. The contents of the .ssh folder and the folder itself should not be writable to anybody but you.