Get started

Overview

Exercises: 20 min
Questions
  • How do I connect to UPPMAX?
  • How do I get the data and tools necessary for the course?
Objectives
  • Connect to UPPMAX
  • Get all the data necessary and the tools running for the course

Foreword:

We will for all exercises use data for the fruit fly, Drosophila melanogaster, as that is one of the currently best annotated organisms and there is plenty of high quality data available. However, working on eukaryotes can be time consuming. Even a small genome like Drosophila would take too long to run within the time we have for this course. Thus to be sure to perform the practicals in good conditions, we will use the smallest chromosome of the drosophila (chromosome 4) like it was a whole genome.

Prerequisites

Connection to Uppmax

Please connect yourself to Uppmax following those instruction UPPMAX login instructions.

Install dependencies (the GAAS repository through dedicated environment)

Once connected you will need you to clone and install our github repository indeed this repository contains NBIS annotation team scripts and will be used during this pratical.

  mkdir -p ~/git ; cd ~/git
  git clone https://github.com/NBISweden/GAAS.git
  cd GAAS
  make install
  source ~/git/GAAS/profiles/activate_rackham_env

Now the GAAS environment is displayed at the beginnin of each prompt line: (GAAS) To get out of the nbis environment and restore your previous environment type:

  deactivate

To reactivate he GAAS environment at any time, just type:

   source ~/git/GAAS/profiles/activate_rackham_env

Setup your general working place

Then you will prepare your general working place.

  • Move to the place where you will work
   cd /proj/g2019006/nobackup/
  • Create your private place where all the magic will happen.
   mkdir $USER
   cd $USER
  • get the data
    Data needed for the exercices have to be copied locally.
   cp -r /sw/courses/annotation/2019/data .