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Genepool Training and Tutorials

This is a summary page for the trainings and tutorial sessions that have been given at the JGI.  

Recordings of talks can be found at this link.


  • New-User-Training-Jun2018.pptx | PowerPoint file
    Training session for JGI staff new to NERSC computing resources. Delivered by Dan Udwary on June 14, 2018.
  • Advanced-Anaconda.pdf | Adobe Acrobat PDF file
    Training session given by Dan Udwary and Mario Melara on June 7, 2018 at JGI. Covers some tips and tricks for working with Anaconda environments, and introduces the basics of packaging software for upload to the Anaconda Cloud.
  • How-to-Break-NERSC.pdf | Adobe Acrobat PDF file
    A talk on the roadmap for JGI computing with NERSC, and best and worst practices. Delivered March 22, 2018 by Dan and Tony.
  • Anaconda-tutorial-11-30-2017.pptx | PowerPoint file
    How and why you should look at the Anaconda software manager as a replacement for the module system. Given at the JGI on 11-30-2017
  • JGI-Modules-Tutorial-2017-11-30.pdf | Adobe Acrobat PDF file
    How and why (or why not) to build modules. Given at the JGI on 11/30/2017.
  • SLURMWorkshop-Sep2017.pptx | PowerPoint file
    Intro slides for the Slurm Workshop conducted at JGI on Sept 28, 2017.
  • SLURMTraining-Aug2017.pptx | PowerPoint file
    Slides from a training session provided by NERSC on August 24 and 31, 2017. Covers the expected timeline for transition to Denovo, the state of JGI computing, SLURM, job accounting.
  • JGI-TFtraining-Jun2017.pptx | PowerPoint file
    Slides for a TaskFarmer training session given to the JGI on June 28, 2017. TaskFarmer is a simple workflow manager.
  • Burst-Buffer-tutorial.pdf | Adobe Acrobat PDF file
    Slides from the training given at the JGI on June 28th 2017. The Burst Buffer is a high-performance disk that can be used to accelerate jobs on Cori.
  • JGItutorial-Jun2017.pptx | PowerPoint file
    A quick guide to the computing resources available to JGI users from NERSC, and getting started on using them. Presentation given June 8, 2017 by Dan Udwary.
  • Advanced-Gitlab.pdf | Adobe Acrobat PDF file
    A tutorial on best practices and advanced features of Git and Gitlab for managing software, working in teams, building Docker images and deploying them automatically. Given at the JGI on May 31st 2017
  • Anaconda-tutorial-4-26-17.pptx | PowerPoint file
    A training session held on April 26, 2017, instructing use of the the Anaconda Python distribution and associated software.
  • JGI-Future-of-Genepool-3-17-2017.pptx | PowerPoint file
    A quick overview of the changes coming to Genepool given by Dan Udwary on March 17, and why moving bioinformatics software to containers will be a critical part of that change.
  • SLURMTraining-Oct13-2016.pptx | PowerPoint file
    Slides from the JGI SLURM workshop held on October 13, 2016.
  • BLASTtutorial-dec2015.pdf | Adobe Acrobat PDF file
    Dan Udwary gave a training on using BLAST optimally on the Genepool system.
  • 2017-02-06-Gitlab-CI.pdf | Adobe Acrobat PDF file
    A hands-on introduction to Gitlab, a Continuous Integration platform, from Feb. 6th 2017
  • Git-+-Docker-Tutorial-Dec01-2016.pdf | Adobe Acrobat PDF file
    Slides from the basic intro to Git and Docker at the JGI, December 1st 2016
  • Docker-for-reproducible-pipelines.pptx | PowerPoint file
    A presentation given by Tony Wildish on March 17 2017, describing NERSC's recommendations for converting JGI pipelines from the Genepool module system to more reproducible Containerized pipelines that can run on Denovo, Cori, and the cloud.
  • Google-Cloud-Training.pptx | PowerPoint file
    A hands-on workshop presented at the JGI, and at the JGI User Meeting in March 2017. Instructs the user in the use of Docker containers and virtual machines in the Google Cloud.