README.md

In selkamand/utilitybeltcavatica: What the Package Does (One Line, Title Case)

utilitybeltcavatica

A bunch of helper functions for working with the sbg cavatica platform

Installation

install.packages("remotes") # Can skip if you already have 'remotes' package installed
remotes::install_github("selkamand/utilitybeltcavatica")

Usage

This package extends functionality of the sevenbridges package on bioconductor.

Getting Started with Sevenbridges

Set up cavatica credentials

Create a new file at: ~/.sevenbridges/credentials

Add the following contents:

[default]
api_endpoint = https://cavatica-api.sbgenomics.com/v2
auth_token   = my_cav_auth_token

my_cav_auth_token can be generated from web interface (hosted here):

Load Libraries

Jump into R load up the libraries we need

library(sevenbridges)   # This library is automatically installed when you install this package
library(utilitybeltcavatica)

Connect to your project of interest

First lets list all all our projects

a <- Auth(from="file",platform = "cavatica")

message("\nPossible Projects:")
a$project()

Then choose one of these to connect to:

project <- a$project(id = "my_project_id")

message("\nProject Selected:")
project

Now we're all set to start using any functions in either the sevenbridges or utilitybeltcavatica packages. Examples of the latter are described below.

Find File By FilePath

All functions described bellow are vectorised

 # Get File Object
find_file_using_filepath(project, filepath)

# Get File Identifier
find_fileid_using_filepath(project, filepath)

selkamand/utilitybeltcavatica documentation built on April 26, 2023, 4:18 p.m.