Introduc*on to Galaxy

Transcription

1 PlateForMe Introduc*on to Galaxy PlateForMe Stéphanie Le Gras

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

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

4 ANALYZING BIOLOGICAL DATA WITH INFORMATICS TOOLS 4

5 PlateForMe Bioinforma*cs analyses Informa*cs data 5

6 Bioinforma*cs analyses Scripts, sokwares Command line 6

7 Bioinforma*cs analyses 7

8 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

9 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

10 Galaxy? 10

11 Galaxy 11

12 GALAXY PROJECT 12

13 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

14 This is Galaxy 14

15 Running analyses with tools 15

16 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

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

18 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

19 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)

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

21 DESCRIPTION OF THE MAIN FEATURES OF GALAXY 21

22 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

23 Top menu Manage your user account Log in/out 23

24 Top menu Find help 24

25 Top menu Run analyses 25

26 Run analysis / tool panel Tool categories TOOL PANEL 26

27 Run analysis / tool panel Tool categories Tools 27

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

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

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

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

32 Get data: data libraries 32

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

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

35 Get data: external data 35

36 Get data: external data 36

37 Get data: external data 37

38 Get data: external data 38

39 Get data: external data 39

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

41 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

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

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

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

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

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

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

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

49 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

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

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

52 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

53 Look up to the History 53

54 Look up to the History 54

55 Dele*ng a dataset 55

56 Dele*ng a dataset 56

57 Dele*ng a dataset 57

58 Dele*ng a dataset 58

59 Dele*ng a dataset 59

60 Dele*ng a dataset 60

61 Dele*ng a dataset 61

62 Workflow Run Workflows 62

63 Workflow 63

64 Workflow 64

65 Workflow 65

66 66

67 Workflow Select input datasets Set parameters Run analysis 67

68 HANDS- ON DATA 68

69 Let s start using Galaxy Go to the Galaxy planorm: hcp:// 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

70 For your attention 70