Setup

Requirements

Nextflow can be used on any POSIX compatible system (Linux, OS X, etc). It requires Bash and Java 11 (or later, up to 18) to be installed.

Optional requirements:

Steps to launch the AWS cloud 9 environment

For this tutorial, we will use the AWS Cloud 9 virtual environment.

Below we included the list with all the users name created that you need together with the CBCRG account ID to sign in the AWS console and launch the environment.

  1. Open this address on your browser: https://eu-west-1.console.aws.amazon.com/cloud9/home

  2. Once you are in the AWS login page, select IAM USER and please fill the credentials below:

    Account ID: 885800555707

    IAM user name: Check this google spreadsheet to check the user assigned to you (under the user column).

    Password: provided by the organization during the session.

  3. When you access the AWS Cloud main page you will find your environment listed in the home page, just click on the Open IDE button and your environment will be launched.

Training materials download and environment setup

Once you launched the environment, download the training materials running the command below on the terminal window that you will find at the button of the IDE:

aws s3 sync s3://cbcrg-eu/atacseq-training-bovreg/setup ./setup/

source setup/all.sh

aws s3 sync s3://cbcrg-eu/atacseq-training-bovreg/config ./config/

Nextflow Installation

Install the latest version of Nextflow copy & pasting the following snippet in a terminal window:

curl https://get.nextflow.io | bash
mv nextflow ~/bin

Check the correct installation running the following command:

nextflow info