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Adds tutorials shared in Slack in GutHub for longevity #43

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cgpu opened this issue Nov 9, 2020 · 2 comments
Open
6 tasks

Adds tutorials shared in Slack in GutHub for longevity #43

cgpu opened this issue Nov 9, 2020 · 2 comments
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@cgpu
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cgpu commented Nov 9, 2020

I am self-assigning me for most tutorials shared in Slack in GutHub for longevity, happy to share the tutorials write up if someone offers to contribute as well.

Tutorials that shouldn't be forgotten after the codeathon:

  • github I: Contribution etiquette issues for tracking tasks, pull requests (authors and reviewers perspective)
  • github II: Command line git commands for developing and pushing code to githhub. How to resolve conflicts and keep branches in sync when many people contribute.
  • conda: Basic commands for managing dependencies, including creating, activating envs and finding and installing packages
  • docker: Finding, building and using docker images/containers. Setting up a DockerHub account, docker login from the command line. Template duo of Dockerfile, environment.yml
  • zenodo: Creating a record and updating the record with revisions from the user interface. Retrieving https links for all files in a zenodo record
  • nextflow: The anatomy of a Nextflow process. Resources for further reading, such as Nextflow patterns. How to define number of cpus or container per process type.
@cgpu cgpu self-assigned this Nov 9, 2020
@adeslatt
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adeslatt commented Nov 9, 2020

  • Shell Basics: Give basic shell instructions.
  • CloudOS Onboarding: Creating the basics of getting on, how CloudOS is priced for researchers, academics, and pharma <- knowing that researchers can plan on their work with this platform will help understand how things work.
  • STRIDES Initiative: Understanding this NIH initiative -- taking people off of their desktop into the collaborative world of the cloud.
  • Organizational Suggestions: Thinking outside of a single program that is modular, into a larger world where you are stitching together your steps - and understanding that each of these individual steps may be spawned into a larger compute - taking full advantage of elastic compute. Data flow model - where things fan out from the start and fan back in. Each individual step maybe a repurposed existing step - tried and true -- now assembled in unique ways to get a new job done.
  • Understanding the Job to be done: What is the problem you are solving? What is the current best practice? How to discover well vetted ways of others. Leveraging with attribution that work.

@adeslatt adeslatt self-assigned this Nov 9, 2020
@gsheynkman
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@cgpu I'm interested in contributing - happy to share where I was confused and what information could be presented to get the uninitiated up to speed. There are two aspects to the feedback - information that is needed and information that is not needed (e.g., details that can be saved for later once someone is comfortable in the environment).

I would be very interested in these tutorials.

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