2. Your environment

In the pico environment, a scheduler system will queue your jobs and execute them as soon as there are free nodes, based on the resources (threads, memory, wall-time) that you specified. The commands for all the processes that you need to run should be written into a shell script file and submitted to the scheduler. You should open a file with a text editor (for example vi, nano or pico), and write at the beginning of the file a header similar to the following:

 #/bin/bash
 #PBS -l walltime=4:00:00
 #PBS -l select=1:ncpus=4:mpiprocs=1:mem=16GB
 #PBS -A <your account>
 #PBS -W group_list="<your account>"

Then, in the body of the script you should first load the appropriate modules. In the pico environment, several bioinformatics modules are ready be loaded. You need first to load two profiles containing prerequisites for some of the available software, by typing in the script: module load profile/bio module load profile/advanced After that, you could write Unix commands, calls to installed software, and so on. Alternatively, you can run commands and software from the command line. Unless you log in into pico using an interactive shell, the pico front end has stringent limits to the process that you run from command line. In this tutorial some short processes can be run from command line, while other requiring more resources will be run through the scheduler. Once you log in into the pico front end, you can load the needed profiles by typing the following commands ($ is the shell prompt, press enter after each command):

 $ module load profile/bio
 $ module load profile/advanced

Now all available modules are ready to be loaded.