training-rstudio-binder

This repository holds the files to create a custom computing environment, or Binder, with data and software that can be used in workshops offered by the Common Fund Data Ecosystem.

Click the to generate a Binder from the data branch of this repository.

Different Binders on Differnt Branches

• The binder on the basic-rstudio branch only has R installed:

• The binder on the rstudio-snakemake-workflow branch has R, snakemake-minimal, and some variant calling software.

• The binder on the conda-workshop-march2021 branch has Rstudio and example code files for conda workshop.

• The binder on the data branch has all the data files used in UNIX workshops

• The binder on the recount3 branch has many R packages from CRAN and Bioconductor

Adding new binders from this repo

For CFDE trainers: if you'd like to build a new Rstudio binder with other installations from this repo -

1. create a new branch
2. edit environment.yml file in the ./binder directory
3. build a new binder - remember to enter the correct Github branch!
4. add the binder badge + brief description to this readme doc (including the repo branch)

Important reminders:

• r-base or some r package (e.g., r-ggplot2) needs to be in the environment.yml file so that R is installed during binder build
• in the pangeo binder form:
  • specify Github branch to point binder to
  • change "Path to a notebook file (optional)" dropdown to "URL" from "File". Type rstudio so the binder opens Rstudio.
• do not merge branches to main or delete branches that existing binders are pointing to, otherwise those binders will not work anymore!