Genomics Workshop Overview: Setup

Overview

This workshop is designed to be run on Cocalc (at UU), but can also be run on pre-imaged Amazon Web Services (AWS) instances. All of the data and most of the software used in the workshop have been moved from Amazon to cocalc. Some additional software, detailed below, must be installed on your computer if you want to use the AWS instance or if you want to install the software to run locally.

If you use Cocalc (recommended for this UU course), only a webbrowser is needed and blow software install can be skipped!
If you do not have spreadsheet software (Excel or Libre Office) please only install Libre Office (instructions below).

Please follow the instructions below to prepare your computer for the workshop:

Required additional software

This lesson requires a working spreadsheet program. If you don’t have a spreadsheet program already, you can use LibreOffice. It’s a free, open source spreadsheet program. Directions to install are included for each Windows, Mac OS X, and Linux systems below.
For local installs for Windows, you will additionally need to install either Git Bash, PuTTY, or the Ubuntu Subsystem.

Windows

  • Install LibreOffice by going to the installation page. The version for Windows should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Once the installer is downloaded, double click on it and LibreOffice should install.
  • Download the Git for Windows installer. Run the installer and follow the steps below:
    • Click on “Next” four times (two times if you’ve previously installed Git). You don’t need to change anything in the Information, location, components, and start menu screens.
    • From the dropdown menu select “Use the Nano editor by default” (NOTE: you will need to scroll up to find it) and click on “Next”.
    • On the page that says “Adjusting the name of the initial branch in new repositories”, ensure that “Let Git decide” is selected. This will ensure the highest level of compatibility for our lessons.
    • Ensure that “Git from the command line and also from 3rd-party software” is selected and click on “Next”. (If you don’t do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the “Git from the command line and also from 3rd-party software” option.)
    • Ensure that “Use the native Windows Secure Channel Library” is selected and click on “Next”.
    • Ensure that “Checkout Windows-style, commit Unix-style line endings” is selected and click on “Next”.
    • Ensure that “Use Windows’ default console window” is selected and click on “Next”.
    • Ensure that “Default (fast-forward or merge) is selected and click “Next”
    • Ensure that “Git Credential Manager Core” is selected and click on “Next”.
    • Ensure that “Enable file system caching” is selected and click on “Next”.
    • Click on “Install”.
    • Click on “Finish”.
    • Check the settings for you your “HOME” environment variable.
      • If your “HOME” environment variable is not set (or you don’t know what this is):
      • Open command prompt (Open Start Menu then type cmd and press [Enter])
      • Type the following line into the command prompt window exactly as shown: setx HOME "%USERPROFILE%"
      • Press [Enter], you should see SUCCESS: Specified value was saved.
      • Quit command prompt by typing exit then pressing [Enter]
  • An alternative option is to install PuTTY by going to the the installation page. For most newer computers, click on putty-64bit-X.XX-installer.msi to download the 64-bit version. If you have an older laptop, you may need to get the 32-bit version putty-X.XX-installer.msi. If you aren’t sure whether you need the 64 or 32 bit version, you can check your laptop version by following the instructions here. Once the installer is downloaded, double click on it, and PuTTY should install.
  • Another alternative option is to use the Ubuntu Subsystem for Windows. This option is only available for Windows 10 - detailed instructions are available here.

Mac OS X

  • Install LibreOffice by going to the installation page. The version for Mac should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Once the installer is downloaded, double click on it and LibreOffice should install.

Linux

  • Install LibreOffice by going to the installation page. The version for Linux should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Once the installer is downloaded, double click on it and LibreOffice should install.

Option A: Using the lessons with Amazon Web Services (AWS)

If you are signed up to take a Genomics Data Carpentry workshop, you do not need to worry about setting up an AMI instance. The Carpentries staff will create an instance for you and this will be provided to you at no cost. This is true for both self-organized and centrally-organized workshops. Your Instructor will provide instructions for connecting to the AMI instance at the workshop.

If you would like to work through these lessons independently, outside of a workshop, you will need to start your own AMI instance. Follow these instructions on creating an Amazon instance. Use the AMI ami-04b3bc83255f918b0 (Data Carpentry Genomics with R 4.0) listed on the Community AMIs page. Please note that you must set your location as N. Virginia in order to access this community AMI. You can change your location in the upper right corner of the main AWS menu bar. The cost of using this AMI for a few days, with the t2.medium instance type is very low (about USD $1.50 per user, per day). Data Carpentry has no control over AWS pricing structure and provides this cost estimate with no guarantees. Please read AWS documentation on pricing for up-to-date information.

If you’re an Instructor or Maintainer or want to contribute to these lessons, please get in touch with us team@carpentries.org and we will start instances for you.

Option B: Using the lessons on your local machine

While not recommended, it is possible to work through the lessons on your local machine (i.e. without using AWS). To do this, you will need to install all of the software used in the workshop and obtain a copy of the dataset. Instructions for doing this are below.

Data

The data used in this workshop is available on FigShare. Because this workshop works with real data, be aware that file sizes for the data are large. Please read the FigShare page linked below for information about the data and access to the data files.

FigShare Data Carpentry Genomics Beta 2.0

More information about these data will be presented in the first lesson of the workshop.

Software

Software Version Manual Available for Description
FastQC 0.11.7 Link Linux, MacOS, Windows Quality control tool for high throughput sequence data.
Trimmomatic 0.38 Link Linux, MacOS, Windows A flexible read trimming tool for Illumina NGS data.
BWA 0.7.17 Link Linux, MacOS Mapping DNA sequences against reference genome.
SAMtools 1.9 Link Linux, MacOS Utilities for manipulating alignments in the SAM format.
BCFtools 1.8 Link Linux, MacOS Utilities for variant calling and manipulating VCFs and BCFs.
IGV Link Link Linux, MacOS, Windows Visualization and interactive exploration of large genomics datasets.

QuickStart Software Installation Instructions

These are the QuickStart installation instructions. They assume familiarity with the command line and with installation in general. As there are different operating systems and many different versions of operating systems and environments, these may not work on your computer. If an installation doesn’t work for you, please refer to the user guide for the tool, listed in the table above.

We have installed software using miniconda. Miniconda is a package manager that simplifies the installation process. Please first install miniconda3 (installation instructions below), and then proceed to the installation of individual tools.

Miniconda3

MacOS

To install miniconda3, type:

$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
$ bash Miniconda3-latest-MacOSX-x86_64.sh

Then, follow the instructions that you are prompted with on the screen to install Miniconda3.

FastQC

MacOS

To install FastQC, type:

$ conda install -c bioconda fastqc=0.11.7=5

FastQC Source Code Installation

If you prefer to install from source, follow the directions below:

$ cd ~/src
$ curl -O http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip
$ unzip fastqc_v0.11.7.zip

Link the fastqc executable to the ~/bin folder that you have already added to the path.

$ ln -sf ~/src/FastQC/fastqc ~/bin/fastqc

Due to what seems a packaging error the executable flag on the fastqc program is not set. We need to set it ourselves.

$ chmod +x ~/bin/fastqc

Test your installation by running:

$ fastqc -h

Trimmomatic

MacOS

conda install -c bioconda trimmomatic=0.38=0

Trimmomatic Source Code Installation

If you prefer to install from source, follow the directions below:

$ cd ~/src
$ curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
$ unzip Trimmomatic-0.38.zip

The program can be invoked via:

$ java -jar ~/src/Trimmomatic-0.38/trimmomatic-0.38.jar

The ~/src/Trimmomatic-0.38/adapters/ directory contains Illumina specific adapter sequences.

$ ls ~/src/Trimmomatic-0.38/adapters/

Test your installation by running: (assuming things are installed in ~/src)

$ java -jar ~/src/Trimmomatic-0.38/trimmomatic-0.38.jar

Simplify the Invocation, or to Test your installation if you installed with miniconda3:

To simplify the invocation you could also create a script in the ~/bin folder:

$ echo '#!/bin/bash' > ~/bin/trimmomatic
$ echo 'java -jar ~/src/Trimmomatic-0.36/trimmomatic-0.36.jar $@' >> ~/bin/trimmomatic
$ chmod +x ~/bin/trimmomatic

Test your script by running:

$ trimmomatic

BWA

MacOS

conda install -c bioconda bwa=0.7.17=ha92aebf_3

BWA Source Code Installation

If you prefer to install from source, follow the instructions below:

$ cd ~/src
$ curl -OL http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2
$ tar jxvf bwa-0.7.17.tar.bz2
$ cd bwa-0.7.17
$ make
$ export PATH=~/src/bwa-0.7.17:$PATH

Test your installation by running:

$ bwa

SAMtools

MacOS

$ conda install -c bioconda samtools=1.9=h8ee4bcc_1

SAMtools Versions

SAMtools has changed the command line invocation (for the better). But this means that most of the tutorials on the web indicate an older and obsolete usage.

Using SAMtools version 1.9 is important to work with the commands we present in these lessons.

SAMtools Source Code Installation

If you prefer to install from source, follow the instructions below:

$ cd ~/src
$ curl -OkL https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
$ tar jxvf samtools-1.9.tar.bz2
$ cd samtools-1.9
$ make

Add directory to the path if necessary:

$ echo export `PATH=~/src/samtools-1.9:$PATH` >> ~/.bashrc
$ source ~/.bashrc

Test your installation by running:

$ samtools

BCFtools

MacOS

$ conda install -c bioconda bcftools=1.8=h4da6232_3

BCF tools Source Code Installation

If you prefer to install from source, follow the instructions below:

$ cd ~/src
$ curl -OkL https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2
$ tar jxvf bcftools-1.8.tar.bz2
$ cd bcftools-1.8
$ make

Add directory to the path if necessary:

$ echo export `PATH=~/src/bcftools-1.8:$PATH` >> ~/.bashrc
$ source ~/.bashrc

Test your installation by running:

$ bcftools

IGV