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RO-Crate x GA4GH Cloud

The [Reserch Object Crate (RO-Crate)][org-ro-crate] and [Global Alliance for Genomics and Health (GA4GH)][org-ga4gh] communities both propose schemas to represent computational analysis workflows with the [Workflow RO-Crate (WROC)][spec-wroc] and [Tool Registry Service (TRS) API][spec-trs] specifications, respectively.

Apart from the workflows themselves, it is also important to be able to adequately describe individual runs of a workflow, i.e., roughly speaking,

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Intro to Programming: Q&A tutorial session, Dec 9th, 2021

---

13:20:50 From Linnea: I just wanted to ask how we should name the file in our code - so that you dont have to alter it when you take the single tasks. Sequence or seq.fa?

@Linnea: It looks like you are speaking about the input file? It shouldn't matter because we will test your functions individually, not the whole code together. Specifically, we will import your function definitions and pass in whatever inputs we want. It is important though that you use the function definitions exactly in the way that we defined them, do not change the function names or argument names. It is okay to add additional arguments, as long as you provide some defaults for them.

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FASP Demonstrator @ GA4GH Plenary 2020: Input Data

Metadata file

name: thousand_genomes_meta.csv
size: 780047
checksums:
  MD5: 0238926f1ff7d62d7052a432968dd379
  CRC32c: 39BE9FFD

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FASP Demonstrator @ GA4GH Plenary 2020: Input Data DRS-Filer Payloads

Metadata

AWS

{
  "access_methods": [
    {

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Error handling across GA4GH Cloud specs

Date: 24-MAY-2020

WES

'400':
  description: The request is malformed.
  schema:

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def __handle_task_not_found(exception: Exception) -> Response:
    return Response(
        response=dumps({
            'msg': 'The requested task was not found.',
            'status_code': '404'
            }),
        status=404,
        mimetype="application/problem+json"
    )

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~/.bashrc

Bash prompt

To use, overwrite the default definitions of PS1 in ~/.bashrc.

Includes conda and virtualenv environments as well as the current git branch, if any. Set changeps1: false in ~/.condarc and add export VIRTUAL_ENV_DISABLE_PROMPT=1 to ~/.bashrc to to disable the default prompt modifications by conda and virtualenv, respectively.

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Product submission instructions

References

• Work Product Submission Guidelines

Synopsis

• Create a GitHub Gist
• Update the documentation of each repo you have worked on