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Setup
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Running the lessons on your local machine

There are three items that you need to download:

  1. The training material.
  2. The training dataset.
  3. The workshop scripts.

Training material

Download the training material copy & pasting the following command in the terminal:

$ git clone https://github.com/ggrimes/nf-training
$ cd nf-training

{: .language-bash}

Training software

The simplest way to install the software for this course is using conda.

To install conda see here.

To create the training environment run:

conda env create -f environment.yml

{: .language-bash}

Then activate the environment by running

conda activate nf-training

{: .language-bash}

Training scripts

To aid in the delivery of the lesson, the scripts mentioned in each episode, can be found in the respective episode folders in the github repository.

https://github.com/carpentries-incubator/workflows-nextflow/tree/gh-pages/files/scripts

Data

Inside the nf-training folder download the workshop dataset from Figshare, https://figshare.com/articles/dataset/RNA-seq_training_dataset/14822481

$ wget --content-disposition https://ndownloader.figshare.com/files/28531743

{: .language-bash}

Unpack gzipped tar file:

$ tar -xvf  data.tar.gz
$ rm data.tar.gz

{: .language-bash}

Atom text editor setup

Any text editor can be used to write Nextflow scripts. A recommended text editor is Atom.

Go to https://atom.io and you should see a download button. The button or buttons should be specific to your platform and the download package should be installable.

MacOS

Atom follows the standard Mac zip installation process. You can either press the download button from the https://atom.io site or you can go to the Atom releases page to download the atom-mac.zip file explicitly. Once you have that file, you can click on it to extract the application and then drag the new Atom application into your "Applications" folder.

Nextflow language support in Atom

You can add Nextflow language support in Atom by clicking the install button on the atom package site https://atom.io/packages/language-nextflow.

Atom terminal package

https://atom.io/packages/atom-ide-terminal

You can enable a terminal window within Atom by installing the atom-ide-terminal package from https://atom.io/packages/atom-ide-terminal. Click the install button and follow the instructions.

Once installed enable the terminal window by selecting the Packages menu -> Atom IDE terminal -> Toggle menu item.

Nextflow install without conda

Nextflow can be used on any POSIX compatible system (Linux, OS X, etc). It requires Bash and Java 8 (or later, up to 12) to be installed.

Windows systems may be supported using a POSIX compatibility layer like Cygwin (unverified) or, alternatively, installing it into a Linux VM using virtualization software like VirtualBox or VMware.

Nextflow installation

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

# Make sure that Java v8+ is installed:
java -version

# Install Nextflow
export NXF_VER=20.10.0
curl get.nextflow.io | bash

Add Nextflow binary to your user's PATH:

mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin

{: .language-bash}

Check the correct installation running the following command:

nextflow info

{: .language-bash}

Check the correct installation running the following command:

nextflow info

{: .language-bash}

nf-core/tools installation without conda

Pip

pip install nf-core

{: .language-bash}

{% include links.md %}