study.wranger R package for tidying data in a way compatible with VEuPathDB workflows for EDA loading.
To build a docker image
docker build -t veupathdb/study-wrangler .
Build notes:
- add `–progress=plain` if you want to see the errors more easily
- each `remotes::install_github()` command in the Dockerfile eats into a rate limit for anonymous users at GitHub (60 per hour!) - so if you are playing around with things you almost certainly will hit the limit
- setting up credentials for a higher limit seems not worth the cost
To run in docker:
docker run --rm -ti -e PASSWORD=password -p 8989:8787 veupathdb/study-wrangler # Then in your web browser navigate to localhost:8989 and login with "rstudio" and "password"
To add R functions to the repo (using docker):
docker run --rm -ti -v $PWD:/study.wrangler -e PASSWORD=password -p 8888:8787 veupathdb/study-wrangler
# Then in your web browser navigate to localhost:8888 and login with "rstudio" and "password"
# at the RStudio prompt
> library(devtools)
# then in the file browser:
# 1. navigate into ./study.wrangler directory
# 2. Set As Working Directory (gear icon in file browser)
# 3. (or do `setwd("~/study.wrangler")` in console)
> devtools::test()
# actually just `test()` will work
# If running commands in console, you will need to do
> load_all()
# after making changes in the code.
# To update the documentation and/or NAMESPACE file
> document()
> build(path='dist')
> install()
# Note that we are not committing the man/*.Rd files to the repo at the moment
Alternatively, should also be able to install into local RStudio using “remotes” package (where `v0.0.0.9000` is a version tag in the repo`)
> remotes::install_github('VEuPathDB/[email protected]')