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cfe-lab / MiCall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
https://cfe-lab.github.io/MiCall
GNU Affero General Public License v3.0
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Editing projects.json #425

Open ArtPoon opened 6 years ago

ArtPoon commented 6 years ago

I'm starting to write an R function to make it easier to customize projects.json -- it's currently a bit of a bear to edit manually. Just checking in to avoid duplication of effort.

donkirkby commented 6 years ago

Oh right, we edit those files on the QAI web site, but that's not published in this repository.

Would you consider writing the editor in Python with tkinter to avoid bringing another language into the repository? Just a suggestion, of course.

donkirkby commented 5 years ago

Another option besides a GUI tool would be to build on the fetch_sequences.py script and specify the projects in some higher-level form. Maybe a YAML file that lists the accession numbers to download. After editing the high-level definition file, you could run fetch_sequences.py to generate the detailed definitions in projects.json.

donkirkby commented 4 years ago

This is getting bumped in priority, because the QAI pages that we use to edit the project definitions are not going to be supported in the new version of Ruby. Instead of fixing those, I think we should add an editor to this project.

Options to consider:

  1. Look at what @ArtPoon got working. Last time we checked in, that wasn't ready for sharing. Has that changed, Art?
  2. Build a simple editor using Tkinter, the built-in GUI framework in Python.
  3. Build a slightly prettier editor using PySide2. I have some experience with that framework, and it works pretty well. Could we run it inside the docker image?
  4. If it won't run inside docker, consider using Beeware's briefcase to package it up.
  5. Don't write a GUI tool at all, but write a higher-level project definition file that's easier to maintain.
ArtPoon commented 4 years ago

Sorry no, I haven't had the time to do any work on my student's JavaScript code for manipulating the JSON file.