The Galaxy Docker Project. our hands-on tutorial

Size: px
Start display at page:

Download "The Galaxy Docker Project. our hands-on tutorial"

Transcription

1 The Galaxy Docker Project our hands-on tutorial

2 Preparation docker pull quay.io/bgruening/galaxy:gcc2016 docker pull quay.io/bgruening/galaxy-docs-slurm:gcc2016 git clone -b gcc2016

3 Outline Docker basics Galaxy Docker image (usage) Galaxy Docker (internals) Galaxy flavours Here you will learn the internals of the Docker Galaxy Image. We will show you tips and tricks on how to run the Galaxy Docker Image successfully in production, how to manage updates and how to bind the container to a cluster scheduler. Moreover, you will learn how to create your own Galaxy flavour mixing a variety of different tools and visualisations.

4 Container vs. VM

5 Docker basics

6 Container lifecycle containers vs. image data persistence mounting volumes

7 pull docker pull hello-world docker pull docker/whalesay docker pull bgruening/galaxy-stable:16.01 docker pull quay.io/bgruening/galaxy docker images

8 docker run hello-world run docker run hello-world Hello from Docker. This message shows that your installation appears to be working correctly. To generate this message, Docker took the following steps: 1. The Docker client contacted the Docker daemon. 2. The Docker daemon pulled the "hello-world" image from the Docker Hub. 3. The Docker daemon created a new container from that image which runs the executable that produces the output you are currently reading. 4. The Docker daemon streamed that output to the Docker client, which sent it to your terminal. To try something more ambitious, you can run an Ubuntu container with: $ docker run -it ubuntu bash Share images, automate workflows, and more with a free Docker Hub account: For more examples and ideas, visit:

9 run docker run docker/whalesay cowsay Galaxy % docker run docker/whalesay cowsay Galaxy < Galaxy > \ \ \ ##. ## ## ## == ## ## ## ## === /"""""""""""""""" / === ~~~ {~~ ~~~~ ~~~ ~~~~ ~~ ~ / ===- ~~~ \ o / \ \ / \ \ /

10 run % docker run --help Usage: docker run [OPTIONS] IMAGE [COMMAND] [ARG...] Run a command in a new container -a, --attach=[] --add-host=[] --cpu-shares... -d, --detach -e, --env=[] --entrypoint --env-file=[]... -h, --hostname -i, --interactive --name --net=default... -P, --publish-all -p, --publish=[] --privileged --rm -t, --tty -v, --volume=[]... Attach to STDIN, STDOUT or STDERR Add a custom host-to-ip mapping (host:ip) CPU shares (relative weight) Run container in background and print container ID Set environment variables Overwrite the default ENTRYPOINT of the image Read in a file of environment variables Container host name Keep STDIN open even if not attached Assign a name to the container Connect a container to a network Publish all exposed ports to random ports Publish a container's port(s) to the host Give extended privileges to this container Automatically remove the container when it exits Allocate a pseudo-tty Bind mount a volume

11 Control during startup % docker run -i -t -p 8080:80 -p 8021:21 -p 9002:9002 -v /home/user/galaxy_storage/:/export/ --privileged=true -e "NONUSE=reports" -e "GALAXY_CONFIG_ADMIN_USERS=albert@einstein.gov" -e "GALAXY_CONFIG_MASTER_API_KEY=83D4jaba7330aDKHkakjGa937" -e "GALAXY_CONFIG_BRAND='My own Galaxy flavour'" -e "GALAXY_LOGGING=full" quay.io/bgruening/galaxy

12 exec Run a command in a running container % docker exec <container name> supervisorctl restart galaxy:

13 stop Stop a running container. Sending SIGTERM and then SIGKILL after a grace period % docker stop <container name>

14 build Build an image from a Dockerfile % docker build -t image_name <Dockerfile>

15 ps List containers % docker ps

16 Galaxy Docker Container FTP-Server Webserver Scheduler Process control UI ToolShed ready Interactive Environment ready docker run -i -t -p 8080:80 quay.io/bgruening/galaxy:gcc2016 doi: /zenodo.51627

17 Things to try adding Data integrated FTP server becoming an Admin restart Galaxy using export mounts (persistent data) trouble shooting (logging) installing tools install visualizations (biojs)...

18 Galaxy + SLURM = Running_jobs_outside_of_the_container.md

19 Docker flavours

20 Galactic Flavours NCBI-Blast ChemicalToolBox ballaxy NGS-deepTools Galaxy ChIP-exo Galaxy Proteomics Imaging Constructive Solid Geometry Galaxy for metagenomics Galaxy with the Language Application Grid tools RNAcommender OpenMoleculeGenerator

21 Create your own Flavour # Galaxy - My own flavour # # VERSION 0.1 FROM quay.io/bgruening/galaxy:gcc2016 MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com ENV GALAXY_CONFIG_BRAND deeptools # Install Visualisation # RUN install-biojs msa # Adding the tool definitions to the container ADD my_tool_list.yml $GALAXY_ROOT/my_tool_list.yml # Install deeptools RUN install-tools $GALAXY_ROOT/my_tool_list.yml

22 The tools file api_key: admin galaxy_instance: tools: - name: fastqc owner: devteam tool_panel_section_id: cshl_library_information tool_shed_url: #revisions:

23 Galaxy Flavor Generator

Dockerfile & docker CLI Cheat Sheet

Dockerfile & docker CLI Cheat Sheet Dockerfile & docker CLI Cheat Sheet Table of Contents Introduction 1 1. docker CLI Engine 2 1.1 Container Related s 2 1.2 Image Related s 4 1.3 Network Related s 5 1.4 Registry Related s 6 1.5 Volume Related

More information

Red Hat Containers Cheat Sheet

Red Hat Containers Cheat Sheet Red Hat Containers Cheat Sheet Table of Contents Introduction Commands Key 1. Container Runtime Engine 1.A) Container Related Commands 1.B) Image Related Commands 1.C) Network Related Commands 1.D) Registry

More information

Docker Cheat Sheet. Introduction

Docker Cheat Sheet. Introduction Docker Cheat Sheet Introduction Containers allow the packaging of your application (and everything that you need to run it) in a "container image". Inside a container you can include a base operational

More information

Running Splunk Enterprise within Docker

Running Splunk Enterprise within Docker Running Splunk Enterprise within Docker Michael Clayfield Partner Consultant 03/09/2017 1.1 Forward-Looking Statements During the course of this presentation, we may make forward-looking statements regarding

More information

Introduction to Containers

Introduction to Containers Introduction to Containers Shawfeng Dong Principal Cyberinfrastructure Engineer University of California, Santa Cruz What are Containers? Containerization, aka operating-system-level virtualization, refers

More information

INSTALLATION RUNBOOK FOR Iron.io + IronWorker

INSTALLATION RUNBOOK FOR Iron.io + IronWorker INSTALLATION RUNBOOK FOR Iron.io + IronWorker Application Type: Job processing Application Version: 1.0 MOS Version: 8.0 OpenStack version: Liberty Murano package checksum: Glance image checksum (docker):

More information

Who is Docker and how he can help us? Heino Talvik

Who is Docker and how he can help us? Heino Talvik Who is Docker and how he can help us? Heino Talvik heino.talvik@seb.ee heino.talvik@gmail.com What is Docker? Software guy view: Marriage of infrastucture and Source Code Management Hardware guy view:

More information

Container-based virtualization: Docker

Container-based virtualization: Docker Università degli Studi di Roma Tor Vergata Dipartimento di Ingegneria Civile e Ingegneria Informatica Container-based virtualization: Docker Corso di Sistemi Distribuiti e Cloud Computing A.A. 2018/19

More information

Adding Transparency and Automation into the Galaxy Tool Installation Process

Adding Transparency and Automation into the Galaxy Tool Installation Process Adding Transparency and Automation into the Galaxy Tool Installation Process Enis Afgan Johns Hopkins University Galaxy Team Galaxy Admins Web Meetup August 20, 2015. Outline Installing tools in bulk (i.e.,

More information

Network softwarization Lab session 2: OS Virtualization Networking

Network softwarization Lab session 2: OS Virtualization Networking Network softwarization Lab session 2: OS Virtualization Networking Nicolas Herbaut David Bourasseau Daniel Negru December 16, 2015 1 Introduction 1.1 Discovering docker 1.1.1 Installation Please launch

More information

Unix Processes. What is a Process?

Unix Processes. What is a Process? Unix Processes Process -- program in execution shell spawns a process for each command and terminates it when the command completes Many processes all multiplexed to a single processor (or a small number

More information

MYR-2017 SimulATOR user manual

MYR-2017 SimulATOR user manual MYR-2017 SimulATOR user manual Naïo technologies - Gazebo on Nvidia-Docker - Author : Andreu Joan Version : 1.0.0 Date : 2017/07/11 Copyright : Naïo Technologies 1. Requirements Minimal requirements :

More information

Index. Bessel function, 51 Big data, 1. Cloud-based version-control system, 226 Containerization, 30 application, 32 virtualize processes, 30 31

Index. Bessel function, 51 Big data, 1. Cloud-based version-control system, 226 Containerization, 30 application, 32 virtualize processes, 30 31 Index A Amazon Web Services (AWS), 2 account creation, 2 EC2 instance creation, 9 Docker, 13 IP address, 12 key pair, 12 launch button, 11 security group, 11 stable Ubuntu server, 9 t2.micro type, 9 10

More information

DGX-1 DOCKER USER GUIDE Josh Park Senior Solutions Architect Contents created by Jack Han Solutions Architect

DGX-1 DOCKER USER GUIDE Josh Park Senior Solutions Architect Contents created by Jack Han Solutions Architect DGX-1 DOCKER USER GUIDE 17.08 Josh Park Senior Solutions Architect Contents created by Jack Han Solutions Architect AGENDA Introduction to Docker & DGX-1 SW Stack Docker basic & nvidia-docker Docker image

More information

Best Practices for Developing & Deploying Java Applications with Docker

Best Practices for Developing & Deploying Java Applications with Docker JavaOne 2017 CON7957 Best Practices for Developing & Deploying Java Applications with Docker Eric Smalling - Solution Architect, Docker Inc. @ericsmalling Who Am I? Eric Smalling Solution Architect Docker

More information

SQL Server containers with in-container data

SQL Server containers with in-container data SQL Server containers with in-container data This article provides step-by-step instructions for working with SQL Server containers with databases running in the container s private file system ( in-container

More information

Arup Nanda VP, Data Services Priceline.com

Arup Nanda VP, Data Services Priceline.com Jumpstarting Docker Arup Nanda VP, Data Services Priceline.com My application worked in Dev but not in QA Will it work in production? I need an environment right now No, I can t wait for 2 weeks I just

More information

Building Your First SQL Server Container Lab in Docker

Building Your First SQL Server Container Lab in Docker Building Your First SQL Server Container Lab in Docker Chris Bell Founder WaterOx Consulting, Inc What is Docker? Opensource Technology Allows the packaging of all parts an application needs into one package

More information

INDIGO PAAS TUTORIAL. ! Marica Antonacci RIA INFN-Bari

INDIGO PAAS TUTORIAL. ! Marica Antonacci RIA INFN-Bari INDIGO PAAS TUTORIAL RIA-653549! Marica Antonacci!! marica.antonacci@ba.infn.it! INFN-Bari INDIGO PAAS Tutorial Introductory Concepts TOSCA Ansible Docker Orchestrator APIs INDIGO TOSCA custom types and

More information

Getting Started with Hadoop

Getting Started with Hadoop Getting Started with Hadoop May 28, 2018 Michael Völske, Shahbaz Syed Web Technology & Information Systems Bauhaus-Universität Weimar 1 webis 2018 What is Hadoop Started in 2004 by Yahoo Open-Source implementation

More information

docker & HEP: containerization of applications for development, distribution and preservation

docker & HEP: containerization of applications for development, distribution and preservation docker & HEP: containerization of applications for development, distribution and preservation Sébastien Binet LAL/IN2P3 2015-04-13 S. Binet (LAL) docker-hep 2015-04-13 1 / 16 Docker: what is it? http://www.docker.io/

More information

Set up, Configure, and Use Docker on Local Dev Machine

Set up, Configure, and Use Docker on Local Dev Machine Set up, Configure, and Use Docker on Local Dev Machine Table of Contents Set up, Configure, and Use Docker on Local Dev Machine... 1 1. Introduction... 2 1.1 Major Docker Components... 2 1.2 Tools Installed

More information

An introduction to Docker

An introduction to Docker An introduction to Docker Ing. Vincenzo Maffione Operating Systems Security Container technologies on Linux Several light virtualization technologies are available for Linux They build on cgroups, namespaces

More information

Docker 101 Workshop. Eric Smalling - Solution Architect, Docker

Docker 101 Workshop. Eric Smalling - Solution Architect, Docker Docker 101 Workshop Eric Smalling - Solution Architect, Docker Inc. @ericsmalling Who Am I? Eric Smalling Solution Architect Docker Customer Success Team ~25 years in software development, architecture,

More information

Follow me!

Follow me! Stuff I do Follow me! https://pasztor.at @janoszen About this talk 1. Maintaining your Build Stack 2. Orchestrating your Cluster 3. Pitfalls and Recommendations About this talk 1. Maintaining your Build

More information

Singularity: container formats

Singularity: container formats Singularity Easy to install and configure Easy to run/use: no daemons no root works with scheduling systems User outside container == user inside container Access to host resources Mount (parts of) filesystems

More information

Engineering Robust Server Software

Engineering Robust Server Software Engineering Robust Server Software Containers Isolation Isolation: keep different programs separate Good for security Might also consider performance isolation Also has security implications (side channel

More information

Get Started with SQL Server containers with cloned databases

Get Started with SQL Server containers with cloned databases Get Started with SQL Server containers with cloned databases SQL Server containers with database cloning supports delivery of large, writable SQL Server environments in seconds, with minimal storage requirements.

More information

Dockerfile Best Practices

Dockerfile Best Practices Dockerfile Best Practices OpenRheinRuhr 2015 November 07th, 2015 1 Dockerfile Best Practices Outline About Dockerfile Best Practices Building Images This work is licensed under the Creative Commons Attribution-ShareAlike

More information

Investigating Containers for Future Services and User Application Support

Investigating Containers for Future Services and User Application Support Investigating Containers for Future Services and User Application Support JLAB CNI NLIT 2018 () Overview JLAB scope What is a container? Why are we interested? Platform-as-a-Service (PaaS) for orchestration

More information

Booting a Galaxy Instance

Booting a Galaxy Instance Booting a Galaxy Instance Create Security Groups First time Only Create Security Group for Galaxy Name the group galaxy Click Manage Rules for galaxy Click Add Rule Choose HTTPS and Click Add Repeat Security

More information

Cloud Computing with APL. Morten Kromberg, CXO, Dyalog

Cloud Computing with APL. Morten Kromberg, CXO, Dyalog Cloud Computing with APL Morten Kromberg, CXO, Dyalog Cloud Computing Docker with APL Morten Kromberg, CXO, Dyalog 2 Cloud Computing: Definitions 3 Cloud Computing: Definitions Cloud Computing = "Using

More information

" Qué me estás container?" Docker for dummies

 Qué me estás container? Docker for dummies " Qué me estás container?" Docker for dummies Sara Arjona @sara_arjona Pau Ferrer @crazyserver Developer at Moodle HQ Moodle Mobile developer at Moodle HQ #MootES18 Who uses Docker for development? Who

More information

User Guide Infoblox IPAM Driver for Docker. Version 1.0.1

User Guide Infoblox IPAM Driver for Docker. Version 1.0.1 User Guide Infoblox IPAM Driver for Docker Version 1.0.1 Copyright Statements 2017, Infoblox Inc. All rights reserved. The contents of this document may not be copied or duplicated in any form, in whole

More information

Support for Vanilla Universe Checkpointing. Thomas Downes University of Wisconsin-Milwaukee (LIGO)

Support for Vanilla Universe Checkpointing. Thomas Downes University of Wisconsin-Milwaukee (LIGO) Support for Vanilla Universe Checkpointing Thomas Downes University of Wisconsin-Milwaukee (LIGO) Experimental feature! All features discussed are present in the official 8.5 releases. The Morgridge Institute

More information

Introduction to containers

Introduction to containers Introduction to containers Nabil Abdennadher nabil.abdennadher@hesge.ch 1 Plan Introduction Details : chroot, control groups, namespaces My first container Deploying a distributed application using containers

More information

Presented By: Gregory M. Kurtzer HPC Systems Architect Lawrence Berkeley National Laboratory CONTAINERS IN HPC WITH SINGULARITY

Presented By: Gregory M. Kurtzer HPC Systems Architect Lawrence Berkeley National Laboratory CONTAINERS IN HPC WITH SINGULARITY Presented By: Gregory M. Kurtzer HPC Systems Architect Lawrence Berkeley National Laboratory gmkurtzer@lbl.gov CONTAINERS IN HPC WITH SINGULARITY A QUICK REVIEW OF THE LANDSCAPE Many types of virtualization

More information

Tricks of the Captains. Adrian Mouat. Chief Scientist Container Solutions

Tricks of the Captains. Adrian Mouat. Chief Scientist Container Solutions Tricks of the Captains Adrian Mouat Chief Scientist Container Solutions Tricks of the Captains A hodgepodge of tips for Docker nirvana compiled from the brains in the Docker Captains program. And me. Who

More information

agenda PAE Docker Docker PAE

agenda PAE Docker Docker PAE Docker 2016.03.26 agenda PAE Docker Docker PAE 2 3 PAE PlCloud APP Engine Docker Docker Caas APP 4 APP APP volume images 5 App 6 APP Show Time 7 8 Docker Public DockerHup Private registry push pull AUFS

More information

NetApp Jenkins Plugin Documentation

NetApp Jenkins Plugin Documentation NetApp Jenkins Plugin Documentation Release 2.0 Akshay Patil Aug 22, 2017 Contents 1 Contents 3 1.1 Pre-Requisites.............................................. 3 1.2 Configuration...............................................

More information

Lesson: Web Programming(3) Omid Jafarinezhad Sharif University of Technology

Lesson: Web Programming(3) Omid Jafarinezhad Sharif University of Technology Lesson: Web Programming(3) Omid Jafarinezhad Sharif University of Technology Materials HTTP, JavaScript, CSS, HTML5, ReactJs, Flow, Progressive Web App Golang, NodeJs, MongoDB, PostgreSQL, Redis Docker,

More information

Containerized Cloud Scheduling Environment

Containerized Cloud Scheduling Environment University of Victoria Engineering & Computer Science Co-op Work Term Report Fall 2017 Containerized Cloud Scheduling Environment Department of Physics University of Victoria Victoria, BC Tahya Weiss-Gibbons

More information

Docker und IBM Digital Experience in Docker Container

Docker und IBM Digital Experience in Docker Container Docker und IBM Digital Experience in Docker Container 20. 21. Juni 2017 IBM Labor Böblingen 1 What is docker Introduction VMs vs. containers Terminology v Docker components 2 6/22/2017 What is docker?

More information

Docker Cheat Sheet. Table of Contents. Why Docker

Docker Cheat Sheet. Table of Contents. Why Docker Docker Cheat Sheet https://github.com/sunilake/docker-cheat-sheet.git Table of Contents Why Docker Prerequisites Installation Containers Images Networks Registry and Repository Dockerfile Layers Links

More information

CONTAINERIZING JOBS ON THE ACCRE CLUSTER WITH SINGULARITY

CONTAINERIZING JOBS ON THE ACCRE CLUSTER WITH SINGULARITY CONTAINERIZING JOBS ON THE ACCRE CLUSTER WITH SINGULARITY VIRTUAL MACHINE (VM) Uses so&ware to emulate an en/re computer, including both hardware and so&ware. Host Computer Virtual Machine Host Resources:

More information

Microsoft Cloud Workshop. Containers and DevOps Hackathon Learner Guide

Microsoft Cloud Workshop. Containers and DevOps Hackathon Learner Guide Microsoft Cloud Workshop Containers and DevOps Hackathon Learner Guide September 2017 2017 Microsoft Corporation. All rights reserved. This document is confidential and proprietary to Microsoft. Internal

More information

Getting Started With Containers

Getting Started With Containers DEVNET 2042 Getting Started With Containers Matt Johnson Developer Evangelist @mattdashj Cisco Spark How Questions? Use Cisco Spark to communicate with the speaker after the session 1. Find this session

More information

Processes. CS3026 Operating Systems Lecture 05

Processes. CS3026 Operating Systems Lecture 05 Processes CS3026 Operating Systems Lecture 05 Dispatcher Admit Ready Queue Dispatch Processor Release Timeout or Yield Event Occurs Blocked Queue Event Wait Implementation: Using one Ready and one Blocked

More information

UNIX System Programming Lecture 3: BASH Programming

UNIX System Programming Lecture 3: BASH Programming UNIX System Programming Outline Filesystems Redirection Shell Programming Reference BLP: Chapter 2 BFAQ: Bash FAQ BMAN: Bash man page BPRI: Bash Programming Introduction BABS: Advanced Bash Scripting Guide

More information

~Deep dive into Windows Containers and Docker~

~Deep dive into Windows Containers and Docker~ ~Deep dive into Windows Containers and Docker~ Blog: Twitter: http://www.solidalm.com https://twitter.com/cornellknulst Are we doing the right things? In managing infrastructure? In deployment? Desired

More information

Building A Better Test Platform:

Building A Better Test Platform: Building A Better Test Platform: A Case Study of Improving Apache HBase Testing with Docker Aleks Shulman, Dima Spivak Outline About Cloudera Apache HBase Overview API compatibility API compatibility testing

More information

Midterm Presentation Schedule

Midterm Presentation Schedule Midterm Presentation Schedule October 18 th Aurora, Bash, Sangam October 20 th Flash, Omega, CodeRing October 25th Omni, Aviato, NPComplete Mid Term Presentation Format 25 minutes Be prepared to use the

More information

It s probably the most popular containerization technology on Linux these days

It s probably the most popular containerization technology on Linux these days Docker & Perl What is docker? It s probably the most popular containerization technology on Linux these days It s somewhere between chroot jails and virtual machines. Effectively lightweight virtual machines

More information

Containers. Pablo F. Ordóñez. October 18, 2018

Containers. Pablo F. Ordóñez. October 18, 2018 Containers Pablo F. Ordóñez October 18, 2018 1 Welcome Song: Sola vaya Interpreter: La Sonora Ponceña 2 Goals Containers!= ( Moby-Dick ) Containers are part of the Linux Kernel Make your own container

More information

SQL Server Containers for Developers. Julie Lerman

SQL Server Containers for Developers. Julie Lerman SQL Server Containers for Developers Julie Lerman thedatafarm.com @julielerman JULIE LERMAN Software Coach Microsoft Regional Dir. & MVP about.me/julielerman Cross-platform SQL Server Management for Developers

More information

/ Cloud Computing. Recitation 5 September 27 th, 2016

/ Cloud Computing. Recitation 5 September 27 th, 2016 15-319 / 15-619 Cloud Computing Recitation 5 September 27 th, 2016 1 Overview Administrative issues Office Hours, Piazza guidelines Last week s reflection Project 2.1, OLI Unit 2 modules 5 and 6 This week

More information

Code: Slides:

Code:   Slides: Workshop Resources Code: https://github.com/beekpr/public-workshops Slides: https://tinyurl.com/yc2uo3wk Make sure minikube and kubectl is setup (labs/1-setup-cluster.md has some instructions) Kubernetes

More information

Docker on VDS. Aurelijus Banelis

Docker on VDS. Aurelijus Banelis Docker on VDS Aurelijus Banelis Aurelijus Banelis Software developer aurelijus.banelis.lt aurelijus@banelis.lt Docker on VDS You will learn Why VDS? Why docker? What is docker? Is it possible? Why not?

More information

Docker & why we should use it

Docker & why we should use it Docker & why we should use it Vicențiu Ciorbaru Software Engineer @ MariaDB Foundation * * Agenda What is Docker? What Docker brings to the table compared to KVM and Vagrant? Docker tutorial What is Docker

More information

Android meets Docker. Jing Li

Android meets Docker. Jing Li Android meets Docker Jing Li 1 2 > 50 cities in Europe 3 Developer Story 4 Pain in the Admin provision machines ( e.g. mobile CI ) 5 Containerization vs Virtualization 6 Why Docker? Docker Vagrant Resource

More information

Build your dev environment with Docker.

Build your dev environment with Docker. Build your dev environment with Docker Jonathan Brinley 2 What does your dev environment look like? 3 What does your production environment look like? 4 add_action( 'init', function () { remove_post_type_support(

More information

/ Cloud Computing. Recitation 5 September 26 th, 2017

/ Cloud Computing. Recitation 5 September 26 th, 2017 15-319 / 15-619 Cloud Computing Recitation 5 September 26 th, 2017 1 Overview Administrative issues Office Hours, Piazza guidelines Last week s reflection Project 2.1, OLI Unit 2 modules 5 and 6 This week

More information

FEniCS Containers Documentation

FEniCS Containers Documentation FEniCS Containers Documentation Release 1.0 FEniCS Project Jan 29, 2018 Contents 1 Quickstart 3 2 Introduction 5 2.1 What is Docker?............................................. 5 2.2 Installing Docker.............................................

More information

swiftenv Documentation

swiftenv Documentation swiftenv Documentation Release 1.3.0 Kyle Fuller Sep 27, 2017 Contents 1 The User Guide 3 1.1 Installation................................................ 3 1.2 Getting Started..............................................

More information

A Hands on Introduction to Docker

A Hands on Introduction to Docker A Hands on Introduction to Docker Len Bass A Hands on introduction Introduction to to Docker May 2017 1 4, Len 2017 Bass 2017 Len Bass 1 Setting expectations This is an introduction to Docker intended

More information

Ellexus Container Checker user manual

Ellexus Container Checker user manual Ellexus Container Checker user manual (Version 2.11.0) Ellexus Container Checker automatically generates an I/O report for your Docker application. Quick start Step 1: Purchase a Container Checker AMI

More information

Docker A FRAMEWORK FOR DATA INTENSIVE COMPUTING

Docker A FRAMEWORK FOR DATA INTENSIVE COMPUTING Docker A FRAMEWORK FOR DATA INTENSIVE COMPUTING Agenda Intro / Prep Environments Day 1: Docker Deep Dive Day 2: Kubernetes Deep Dive Day 3: Advanced Kubernetes: Concepts, Management, Middleware Day 4:

More information

/ Cloud Computing. Recitation 5 February 14th, 2017

/ Cloud Computing. Recitation 5 February 14th, 2017 15-319 / 15-619 Cloud Computing Recitation 5 February 14th, 2017 1 Overview Administrative issues Office Hours, Piazza guidelines Last week s reflection Project 2.1, OLI Unit 2 modules 5 and 6 This week

More information

Walkthrough OCCAM. Be on the lookout for this fellow: The callouts are ACTIONs for you to do!

Walkthrough OCCAM. Be on the lookout for this fellow: The callouts are ACTIONs for you to do! Walkthrough OCCAM Be on the lookout for this fellow: The callouts are ACTIONs for you to do! When you see the check mark, compare your work to the marked element Objectives In this presentation you ll

More information

A curated Domain centric shared Docker registry linked to the Galaxy toolshed

A curated Domain centric shared Docker registry linked to the Galaxy toolshed A curated Domain centric shared Docker registry linked to the Galaxy toolshed François Moreews 1, Olivier Sallou 2, Yvan le Bras 2, Marie Grosjean 3, Cyril Monjeaud 2, Thomas Darde 4, Olivier Collin 2,

More information

Automating the Build Pipeline for Docker Container

Automating the Build Pipeline for Docker Container Automating the Build Pipeline for Docker Container Nikolai Reed, Jürgen Walter, and Samuel Kounev University of Würzburg November 9-10, 2017 SSP 2017 Karlsruhe, Germany 08.11.17 2 Reproducibility Problem

More information

Get your own Galaxy within minutes

Get your own Galaxy within minutes Get your own Galaxy within minutes Enis Afgan, Nitesh Turaga, Nuwan Goonasekera GCC 2016 Bloomington, IN Access slides from bit.ly/gcc2016_usecloud Today s agenda Introduction Hands on, part 1 Launch your

More information

USING DOCKER FOR MXCUBE DEVELOPMENT AT MAX IV

USING DOCKER FOR MXCUBE DEVELOPMENT AT MAX IV USING DOCKER FOR MXCUBE DEVELOPMENT AT MAX IV Fredrik Bolmsten, Antonio Milán Otero K.I.T.S. Group at Max IV - 2017 1 OVERVIEW What is Docker? How does it work? How we use it for MxCUBE How to create a

More information

CSE 410: Computer Systems Spring Processes. John Zahorjan Allen Center 534

CSE 410: Computer Systems Spring Processes. John Zahorjan Allen Center 534 CSE 410: Computer Systems Spring 2018 Processes John Zahorjan zahorjan@cs.washington.edu Allen Center 534 1. What is a process? Processes 2. What's the process namespace? 3. How are processes represented

More information

Splunk N Box. Splunk Multi-Site Clusters In 20 Minutes or Less! Mohamad Hassan Sales Engineer. 9/25/2017 Washington, DC

Splunk N Box. Splunk Multi-Site Clusters In 20 Minutes or Less! Mohamad Hassan Sales Engineer. 9/25/2017 Washington, DC Splunk N Box Splunk Multi-Site Clusters In 20 Minutes or Less! Mohamad Hassan Sales Engineer 9/25/2017 Washington, DC Forward-Looking Statements During the course of this presentation, we may make forward-looking

More information

BEST PRACTICES FOR DOCKER

BEST PRACTICES FOR DOCKER BEST PRACTICES FOR DOCKER DG-08863-001 _v001 March 2018 Best Practices TABLE OF CONTENTS Chapter 1. Docker Best Practices with NVIDIA Containers... 1 1.1. Prerequisites... 1 1.1.1. Hello World For Containers...

More information

matross Release SNAPSHOT

matross Release SNAPSHOT matross Release 0.1.0-SNAPSHOT June 01, 2014 Contents 1 Getting Started 3 1.1 What is matross?............................................. 3 1.2 Who is matross for?...........................................

More information

Technical Manual. Software Quality Analysis as a Service (SQUAAD) Team No.1. Implementers: Aleksandr Chernousov Chris Harman Supicha Phadungslip

Technical Manual. Software Quality Analysis as a Service (SQUAAD) Team No.1. Implementers: Aleksandr Chernousov Chris Harman Supicha Phadungslip Technical Manual Software Quality Analysis as a Service (SQUAAD) Team No.1 Implementers: Aleksandr Chernousov Chris Harman Supicha Phadungslip Testers: Kavneet Kaur Reza Khazali George Llames Sahar Pure

More information

Cross platform enablement for the yocto project with containers. ELC 2017 Randy Witt Intel Open Source Technology Center

Cross platform enablement for the yocto project with containers. ELC 2017 Randy Witt Intel Open Source Technology Center Cross platform enablement for the yocto project with containers ELC 2017 Randy Witt Intel Open Source Technology Center My personal problems Why d I even do this? THE multiple distro Problem Yocto Project

More information

Docker Container Logging

Docker Container Logging Docker Container Logging Default logging behavior Docker natively streams STDOUT and STDERR from a container into a built-in logging service. In order to make use of this services, applications must be

More information

What you Need to Know about SQL Server and Docker Containers

What you Need to Know about SQL Server and Docker Containers What you Need to Know about SQL Server and Docker Containers Michael Otey, President, TECA, Inc Moderated By: William Wolf Presenting Sponsors Thank You to Our Presenting Sponsors Empower users with new

More information

Hg Mercurial Cheat Sheet

Hg Mercurial Cheat Sheet Hg Mercurial Cheat Sheet Serge Y. Stroobandt Copyright 2013 2016, licensed under Creative Commons BY-NC-SA This page is work in progress! Much of the explanatory text still needs to be written. Nonetheless,

More information

Harbor Registry. VMware VMware Inc. All rights reserved.

Harbor Registry. VMware VMware Inc. All rights reserved. Harbor Registry VMware 2017 VMware Inc. All rights reserved. VMware Harbor Registry Cloud Foundry Agenda 1 Container Image Basics 2 Project Harbor Introduction 3 Consistency of Images 4 Security 5 Image

More information

Docker on Ubuntu. Install and configure Docker, along with deploying and managing Linux-based containers, on an Ubuntu server.

Docker on Ubuntu. Install and configure Docker, along with deploying and managing Linux-based containers, on an Ubuntu server. Docker on Ubuntu Friday, August 4, 2017 1:48 PM Install and configure Docker, along with deploying and managing Linux-based containers, on an Ubuntu server. This is a short workshop to introduce you to

More information

Introduction to Container Technology. Patrick Ladd Technical Account Manager April 13, 2016

Introduction to Container Technology. Patrick Ladd Technical Account Manager April 13, 2016 Introduction to Container Technology Patrick Ladd Technical Account Manager April 13, 2016 Container Technology Containers 3 "Linux Containers" is a Linux kernel feature to contain a group of processes

More information

Infrastructure at your Service. Oracle over Docker. Oracle over Docker

Infrastructure at your Service. Oracle over Docker. Oracle over Docker Infrastructure at your Service. Infrastructure at your Service. About me David Hueber COO Principal Consultant Mobile +41 79 963 43 68 david-.hueber@dbi-services.com www.dbi-services.com Page 2 18.11.2015

More information

for Devs Christopher M. Judd

for Devs Christopher M. Judd for Devs Christopher M. Judd Christopher M. Judd CTO and Partner at leader lab Docker hub daemon nuez nuez nuez-db nuez-db tomcat 8 user mysql nuez:1.0 nuez-db:1.0 mysql tomcat tomcat 8 tomcat 7 https://github.com/cjudd/nuez

More information

Be smart. Think open source.

Be smart. Think open source. Dockerfiles Be smart. Think open source. Dockerfiles What is a Dockerfile? Build instructions for Docker images Each command creates a layer in the image FROM centos:7 LABEL maintainer="foo.bar@example.com"

More information

The Classical OS Model in Unix

The Classical OS Model in Unix The Classical OS Model in Unix Nachos Exec/Exit/Join Example Exec parent Join Exec child Exit SpaceID pid = Exec( myprogram, 0); Create a new process running the program myprogram. int status = Join(pid);

More information

INFRASTRUCTURE AS CODE

INFRASTRUCTURE AS CODE INFRASTRUCTURE AS CODE David Sherman EQUIPE PLEIADE BORDEAUX SUD-OUEST 2016-11-08 2016-11-08-22 Pets versus Cattle 2016-11-08-23 Pets versus Cattle (or sheep) https://vimeo.com/4486963 2016-11-08-24 Infrastructure

More information

Introduction To. Barry Grant

Introduction To. Barry Grant Introduction To Barry Grant bjgrant@umich.edu http://thegrantlab.org Working with Unix How do we actually use Unix? Inspecting text files less - visualize a text file: use arrow keys page down/page up

More information

Deploying applications to Heterogeneous Hardware using Rancher and Docker

Deploying applications to Heterogeneous Hardware using Rancher and Docker Deploying applications to Heterogeneous Hardware using Rancher and Docker Bruno Grazioli Research Assistant, ZHAW 14th Docker Switzerland User Group Meetup 31st May 2017 Outline Brief introduction to Rancher

More information

Singularity: Containers for High-Performance Computing. Grigory Shamov Nov 21, 2017

Singularity: Containers for High-Performance Computing. Grigory Shamov Nov 21, 2017 Singularity: Containers for High-Performance Computing Grigory Shamov Nov 21, 2017 Outline Software and High Performance Computing: Installation/Maintenance of the HPC Software stack Why containers and

More information

W4118: OS Overview. Junfeng Yang

W4118: OS Overview. Junfeng Yang W4118: OS Overview Junfeng Yang References: Modern Operating Systems (3 rd edition), Operating Systems Concepts (8 th edition), previous W4118, and OS at MIT, Stanford, and UWisc Outline OS definitions

More information

12 (15) Factor App Workshop

12 (15) Factor App Workshop 12 (15) Factor App Workshop http://bit.ly/15factor-uberconf-2018 Christopher M. Judd Christopher M. Judd CTO and Partner at leader 221 BROUGHT TO YOU IN PARTNERSHIP WITH Getting Started With Docker BY

More information

LSST software stack and deployment on other architectures. William O Mullane for Andy Connolly with material from Owen Boberg

LSST software stack and deployment on other architectures. William O Mullane for Andy Connolly with material from Owen Boberg LSST software stack and deployment on other architectures William O Mullane for Andy Connolly with material from Owen Boberg Containers and Docker Packaged piece of software with complete file system it

More information

Docker. Master the execution environment of your applications. Aurélien Dumez. Inria Bordeaux - Sud-Ouest. Tuesday, March 24th 2015

Docker. Master the execution environment of your applications. Aurélien Dumez. Inria Bordeaux - Sud-Ouest. Tuesday, March 24th 2015 Docker Master the execution environment of your applications Aurélien Dumez Inria Bordeaux - Sud-Ouest Tuesday, March 24th 2015 Aurélien Dumez Docker 1 / 34 Content 1 The bad parts 2 Overview 3 Internals

More information

Cloud-Native Applications. Copyright 2017 Pivotal Software, Inc. All rights Reserved. Version 1.0

Cloud-Native Applications. Copyright 2017 Pivotal Software, Inc. All rights Reserved. Version 1.0 Cloud-Native Applications Copyright 2017 Pivotal Software, Inc. All rights Reserved. Version 1.0 Cloud-Native Characteristics Lean Form a hypothesis, build just enough to validate or disprove it. Learn

More information

Neale Ferguson

Neale Ferguson Introduction to Docker & OpenShift Neale Ferguson 2017-06-24 http://download.sinenomine.net/clefos/epel7/getting_started_with_openshift_on_z.pdf Preface Examples built and run using ClefOS 7.3 CentOS Clone

More information

Running Blockchain in Docker Containers Prerequisites Sign up for a LinuxONE Community Cloud trial account Deploy a virtual server instance

Running Blockchain in Docker Containers Prerequisites Sign up for a LinuxONE Community Cloud trial account Deploy a virtual server instance Running Blockchain in Docker Containers The following instructions can be used to install the current hyperledger fabric, and run Docker and blockchain code in IBM LinuxONE Community Cloud instances. This

More information