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coco2019-training's Introduction

Instructions

Install VirtualBox

  • Go to the VirtualBox Download page: https://www.virtualbox.org/wiki/Downloads

  • Select the link from the "VirtualBox 5.2.12 platform packages" section that matches your system.

  • For Windows 10 users:

    1. Double-click the downloaded executable file (Windows Installer 1.1 or higher is required)
    2. Select default options in installation dialog.
    3. The installer will create a "VirtualBox" group in the Windows Start menu.
    4. For more detailed step-by-step instructions, look here
  • For Mac users:

    1. Double-click on the downloaded dmg file to have its contents mounted
    2. A window will open telling you to double click on the VirtualBox.pkg installer file displayed in that window.
    3. This will start the installer, which will allow you to select where to install VirtualBox to.
    4. After installation, you can find a VirtualBox icon in the "Applications" folder in the Finder.
  • For Ubuntu users:

    • Step-by-step instructions can be found here

Download and import the VM image file

  • Download from https://training.repronim.org/reprotraining.ova
  • To import the reprotraining.ova file:
    1. Open VirtualBox on your computer
    2. select "File" -> "Import Appliance" from the VirtualBox menu.
    3. Click through the import wizard dialog leaving the default settings (see here for example step-by-step instructions here).

Starting the VM

  • Open VirtualBox on your computer
  • Choose "reprotraining" from the menu on the left and press "start" (the green arrow) to start the Ubuntu virtual machine.

Issues:

  • if you have a windows 10 pro 64 bit (eg Lenovo X1C) machine and get an error like: vt-x/amd-v hardware acceleration is not available on your system, look here
  • if you are unable to install VirtualBox due to virtualization technology (VT-x) not being enabled on your system, look here

The Presentations

All tutorials and slides are available from the http://www.repronim.org/coco2019-training/ generated from sources within gh-pages branch of this repository.

coco2019-training's People

Contributors

bpoldrack avatar cmtgreenwood avatar djarecka avatar dnkennedy avatar jbpoline avatar jgrethe avatar mih avatar mjtravers avatar satra avatar yarikoptic avatar

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coco2019-training's Issues

TODO: container review on day 2

During the review session on day 2, I would like to show people how to build a singularity image in docker.

a pain point of some HPC users is that they cannot build their images on hpc and don't have singularity on their local machine.

i'll create an image put the dockerhub url here.

Day 1 Docker image

@djarecka @yarikoptic - I made a Docker image with datalad, git, and git-annex, intended to be used for parts of day 1's presentations.

Generated with:

docker run --rm kaczmarj/neurodocker:0.4.3 generate docker \
  --base=neurodebian:stretch \
  --pkg-manager=apt \
  --install datalad git git-annex-standalone

And available on DockerHub as kaczmarj/coco2019:day1.

Intro PPT

There's a slide that says "Think Locally; Act Globally". I may just be missing the joke but the phrase is "Think globally, act locally". (Which makes a better analogy to "Think reproducibly, act re-executably".

Can't submit a PR on a powerpoint, though.

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