vjcitn/anvilbestpractices

Bioconductor practices recommended for working with NHGRI AnVIL

AnVILBestPractices for workspaces involved with interactive analysis in AnVIL

• The workspace code and documentation is managed in a github repository

  • A github action (that will typically be independent of AnVIL's cloud resources) can be used to check or enhance the package on change events
    • The action will "emulate" an AnVIL cloud environment by using an endorsed container image
    • The action will also produce and register a Docker container to ensure that the software employed in the workspace is runnable in the future

• It is recommended that the repository be organized as an R package

  • R packages can be evaluated with automated quality control procedures
  • Package metadata formally defines requirements for associated software tools
  • Documentation of workspace resources can be standardized

• The README.md can be transformed into the workspace "Dashboard" component using AnVILPublish.

  • The README.md should include "badges" to clearly indicate package status to individuals visiting the workspace
  • By using a global https reference to a figure in the github repo, images for the Dashboard can be included:

• Vignette code will be inserted into the "Analyses" component of the workspace by AnVILPublish

anvilbestpractices's Issues

project element: provide options to choose from celldex resources for labeling

add download feature for new classification

introduce the SingleR workflow for labeling a new SCE

speed up miniconda

BASILISK_MINICONDA_VERSION=py311_23.11.0-2 should be noted in Dashboard/readme if zellkonverter will be used

Upload mode selection: local files (fileInput) or files on server (list.files)

Consider whether you want to handle h5ad directly

It means that there has to be a conda installation at least once before the app will work