Introduc*on to Galaxy

PlateForMe Introduc*on to Galaxy PlateForMe Stéphanie Le Gras

Guidelines Analyzing biological data with informa*cs tools Galaxy project Descrip*on of the main features of Galaxy Hands- on 2

Omics need a*cs, inform- a*cs 3

ANALYZING BIOLOGICAL DATA WITH INFORMATICS TOOLS 4

PlateForMe Bioinforma*cs analyses Informa*cs data 5

Bioinforma*cs analyses Scripts, sokwares Command line 6

Bioinforma*cs analyses 7

Bioinforma*cs analyses Program 1 Program 2 Program 3 Program 4 Command line 1 Command line 2 Command line 3 Command line 4 Program n Command line n 8

Workflow tools Cipres ehive Galaxy phylo.org ensembl.org/info/docs/ehive/index.html main.g2.bx.psu.edu Knime knime.org Mobyle mobyle.pasteur.fr Taverna taverna.org.uk 9

Galaxy? 10

Galaxy 11

GALAXY PROJECT 12

What is Galaxy? Galaxy is a compu=ng plaborm that enables people to run complex bioinforma=cs tools on a compute cluster through a simple web interface. 13

This is Galaxy 14

Running analyses with tools 15

Galaxy philosophy Perform, and share complete analysis No programming skills required Open source and free solu*on Very large and ac=ve community Reproducibility/Usability 16

PlateForMe General comments All analyses are run on remote compu*ng infrastructures No need to have a Supercomputer to use Galaxy Web browser 17

PlateForMe How does it work? Your research ins*tute Connect to Galaxy web site through a web browser (hcps://usegalaxy.org/) Download and upload of the data Galaxy instance Run analyses 18

PlateForMe We are not alone Your research ins*tute World wide Download and upload of the data Remote instance of Galaxy 19 Uploading (takes a lot of *me) Shared compu*ng power (longer analysis)

A local instance of Galaxy High availability Fast network access (through Osiris/Renater) Strong compu*ng resources Custom install, tools, genomes Local support 20

DESCRIPTION OF THE MAIN FEATURES OF GALAXY 21

GalaxEast Top menu TOOL PANEL 22 Data display and tools dialog window HISTORY PANEL keep track of each jobs that have been run Grey: job is wai*ng to run Yellow: job is running Green: job is done Red: job encountered a problem

Top menu Manage your user account Log in/out 23

Top menu Find help 24

Top menu Run analyses 25

Run analysis / tool panel Tool categories TOOL PANEL 26

Run analysis / tool panel Tool categories Tools 27

Run analysis / tool panel Tools dialog window - Set parameters - Run tools - Get help on tools 28

Get data: data libraries Get shared data (Shared Data > Data Libraries) 29

Get data: data libraries Click on the data library of interest 30

Get data: data libraries 1. Select the datasets of interest 2. Click on go to import the datasets to current or new history 31

Get data: data libraries 32

Get data: external data Get external data from UCSC (table browser), Ensembl (Biomart), SRA, ModEncode 33

Get data: external data 1. Search for your dataset of interest Ex: SRR566921 34

Get data: external data 35

Get data: your own data Use the tool Get Data/Upload File 40

Get data: your own data 1. Select a file format 2. Browser a file 2. Choose a file imported using FTP server 3. Select a genome 41

Get your own data in Galaxy Use the drag- and- drop u*lity 42

Get your own data in Galaxy 1. Select a file format 3. Always select a genome 43

Look up to the History HISTORY PANEL Keep track of each job run 1 box = 1 job = 1 dataset 44

Look up to the History Grey box: job is wai*ng to run 45

Look up to the History Yellow box: job is running 46

Look up to the History Green box: job is done 47

Look up to the History Red box: job encountered a problem 48

Look up to the History Clicking on the name of the dataset displays informa*on and menus File format Genome name Number of line in the dataset If dataset is a text file, display the first lines of the file 49

Look up to the History Display dataset in middle panel Edit acributes of dataset: Name Format Genome Remove dataset (!) 50

Look up to the History Save dataset in file Rerun the tool with the same parameters 51

Look up to the History History management bucon: Display all histories Create new Share data Extract workflow from history Show/hide deleted dataset Delete dataset, history 52

Look up to the History 53

Look up to the History 54

Dele*ng a dataset 55

Workflow Run Workflows 62

Workflow 63

Workflow 64

Workflow 65

Workflow Select input datasets Set parameters Run analysis 67

HANDS- ON DATA 68

Let s start using Galaxy Go to the Galaxy planorm: hcp://www.galaxy- igbmc.fr/ Login: user[1- >12] Password: training Go to the GalaxEast wiki: hcp://wiki.galaxy- igbmc.fr/doku.php? id=help:introduc*on2galaxy 69

For your attention 70