README.md

• 🔮 rportal - Interacting with the UMCCR Data Portal
  • 🍕 Installation
  • 🌀 CLI
    • Bioinformatics Data Sharing
  • 🚕 Running

🔮 rportal - Interacting with the UMCCR Data Portal

🍕 Installation

devtools::install_github("umccr/rportal")
# remotes::install_github("umccr/rportal")

🌀 CLI

{rportal} currently has one convenience wrapper for generating presigned URLs for bioinformatics data (FASTQs, BAMs, VCFs and HTMLs/TSVs):

Bioinformatics Data Sharing

A datashare.R command line interface is available for convenience. You need to export the rportal/inst/scripts/datashare/ directory to your PATH in order to use datashare.R:

datashare_cli=$(Rscript -e 'x = system.file("scripts/datashare", package = "rportal"); cat(x, "\n")' | xargs)
export PATH="${datashare_cli}:${PATH}"

datashare.R --version
0.1.2 

#-----------------------------------#
datashare.R --help
Usage
=====
 
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rportal/scripts/datashare/datashare.R [options]


Options
=======
--subject_id=SUBJECT_ID
        Subject ID.

--library_id_tumor=LIBRARY_ID_TUMOR
        Library ID of tumor.

--wts
        This is a WTS library.

--csv_output=CSV_OUTPUT
        CSV output path.

--append
        Append to existing file (or write to new one if file does not exist -- caution: no column headers are written).

--version, -v
        Print rportal version and exit.

--help, -h
        Show this help message and exit

🚕 Running

datashare.R \
  --subject_id SBJ0XXXX \
  --library_id_tumor L230XXXX \
  --wts \
  --csv_output urls_SBJ0XXXX_L230XXXX.csv