University of Arizona: May 30-31, 2019

University of Arizona

May 30-31, 2019

8:30am - 5:00pm

Instructors: Erin Becker, François Michonneau, Sarah Stevens, Jason Williams

Helpers: Ryan Bartelme, Upendra Devisetty, Alison Harrington, Cesar Medina, Xue Pan, Sateesh Peri, Travis Struck

General Information

REGISTRATION: Please register at: Google Sheet Registration

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 1500 E University Blvd. Tucson, AZ. Get directions with OpenStreetMap or Google Maps.

When: May 30-31, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

The room is wheelchair / scooter accessible.
Accessible restrooms are available.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email Jason Williams williams@cshl.edu for more information about workshop content and Uwe Hilgert, hilgert@bio5.org for information on local logistics.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Genomics workshop

Day 1

Before starting	Pre-workshop survey
Morning	Project Organization and Management
	Introduction to the Command Line
Afternoon	Data Wrangling and Processing
Evening	END

Day 2

Morning	Introduction to Cloud Computing for Genomics
Morning/Afternoon	Introduction R for Genomics
Evening	Post-workshop survey
	END

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

Project Organization and Management

Introduction to the Command Line

Data Wrangling and Processing for Genomics

Introduction to Cloud Computing for Genomics

Introduction to R for Genomics

R scripts written during the workshop

Setup

To participate in a Data Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything and try opening it to make sure it works before the start of your workshop. If you run into any problems, please feel free to email the instructor or arrive early to your workshop on the first day. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Accounts needed for workshop

This workshop will be hosted using CyVerse resources.

Register for a CyVerse account if you have not already done so at https://user.cyverse.org/.
Request access to Atmosphere: To request access to Atmosphere, login to the CyVerse User Portal (https://user.cyverse.org/). In the Services Menu under ‘MY SERVICES’ you should see Atmosphere listed as an option you can launch. If not, look under the Available menu, and click the ‘REQUEST ACCESS’ link. You will receive an email requesting additional information. To qualify for an Atmosphere account, your CyVerse account must be associated with an institutional email address (e.g. .edu/.org/.gov). For justification, you may comment that you are attending the May 2019 workshop at the University of Arizona. </ul></p>
Platform-specific Notes

This workshop will be using the software outlined in the install instructions below. Please see the section for your operating system for those directions.
Windows

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.
1. A spreadsheet program
2. Putty
3. FTP Client (Filezilla)
4. R
5. IGV
  If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.
  - To download IGV, please visit this page and log in. Please register if you do not already have a login.
  - Click on the large button for the Download Binary Distribution
  - Find the zip archive on your computer and expand it
  - To run IGV, double-click on the IGV.bat file.
Mac

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.
1. A spreadsheet program
  For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
  If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
  - Download the Installer
    Install LibreOffice by going to the installation page. The version for Mac should automatically be selected. Click Download Version 6.0.3 or later. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
  - Install LibreOffice
    Once the installer is downloaded, double click on it and it should install.
  - To use LibreOffice, double click on the icon and it will open.
2. FTP Client (Filezilla)
  An FTP client will help you transfer files easily between your computer and the cloud.
  - Go to the Filezila download page
  - Chose the download link appropriate to your system
  - To use it, double-click on the downloaded file
  - Follow any installation instructions, if any
  - At the workshop we will give you additional information (e.g. host, username, port) to connect
3. R
  In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
  - Go to CRAN and click on Download R for (Mac) OS X
  - Select the .pkg file for the version of OS X that you have and the file will download.
  - Double click on the file that was downloaded and R will install
  - Go to the RStudio Download page
  - Under Installers select RStudio 1.1.447 or later - Mac OS X 10.6+ (64-bit) to download it.
  - Once it's downloaded, double click the file to install it
  - Once it's installed, open RStudio to make sure it works and you don't get any error messages.
4. IGV
Linux

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.
1. A spreadsheet program
  For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
  If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
  - Download the Installer
    Install LibreOffice by going to the installation page. The version for Linux should automatically be selected. Click Download Version 6.0.3 or later. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
  - Install LibreOffice
    Once the installer is downloaded, double click on it and it should install.
  - To use LibreOffice, double click on the icon and it will open.
2. FTP Client (Filezilla)
  An FTP client will help you transfer files easily between your computer and the cloud.
  - Go to the Filezila download page
  - Chose the download link appropriate to your system
  - To use it, double-click on the downloaded file
  - Follow any installation instructions, if any
  - At the workshop we will give you additional information (e.g. host, username, port) to connect
3. R
  In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
  - R is available through most Linux package managers. You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R).
  - To install RStudi, go to the RStudio Download page
  - Under Installers select the version for your distribution.
  - Once it's downloaded, double click the file to install it
  - Once it's installed, open RStudio to make sure it works and you don't get any error messages.
4. IGV
  If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.
  - To download IGV, please visit this page and log in. Please register if you do not already have a login.
  - Click on the large button for the Download Binary Distribution
  - Find the zip archive on your computer and expand it
  - To run IGV, double-click on the IGV.bat file.