hesselberthlab / RNARePore

Direct detection of RNA repair by nanopore sequencing
https://www.biorxiv.org/content/10.1101/2022.05.29.493267v1
2 stars 0 forks source link

Create script to dl & unpack data from Zenodo #5

Closed lkwhite closed 1 year ago

lkwhite commented 1 year ago

JH: We should also add a zenodo_download.sh script at the top level to download and unpack the data into directories so that the Rmds just run.

Possible to use https://cran.r-project.org/web/packages/zen4R/index.html? Need to test it.

lkwhite commented 1 year ago

Whichever option we use, want to write something to organize these into subdirectories to enable easy rolling up of all files in a folder in the R scripts. Sublevels don't appear to be an option in Zenodo dataset uploads.

lkwhite commented 1 year ago

zen4R looks handy but currently can't grab a subset of files in a record.

lkwhite commented 1 year ago

inborutils download_zenodo function works better for me

lkwhite commented 1 year ago

Alright, kludged a solution together in FileDownloader.Rmd. Will need to fix file paths in remaining scripts to match this new organizational scheme.