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GalaxyConnector

About

This package will allow you to interact with any Galaxy instance for which you have an API Key. You can retrieve and upload files from and to Galaxy and save and restore your R Session in a Galaxy history.

Install

To install, use

library(devtools)
install_github("scholtalbers/r-galaxy-connector")

End user

First load the package: library(GalaxyConnector)

Setup keys for all sessions

If you do not want to run gx_init each time you want to communicate with Galaxy, you can set the variables in your ~/.Renviron file.

e.g.

GX_API_KEY=digitsAndCharacters        # Your Galaxy API Key
GX_GALAXY_URL=http://usegalaxy.org    # The Galaxy instance url
GX_HISTORY_ID=digitsAndCharacters     # The Galaxy History ID

Can set the environment variables using R commands:

Sys.setenv("GX_API_KEY" = 'your_Galaxy_API_key')
Sys.setenv("GX_GALAXY_URL" = 'the_galaxy_url')
Sys.setenv("GX_HISTORY_ID" = 'your_history_id')

Initialization

Use gx_init() to setup the current session only (see below for more information).

You can find the API key under user preference in the Galaxy instance.

Initialize the GalaxyConnector: gx_init(API_KEY='your_Galaxy_API_Key', GALAXY_URL='usegalaxy.org', HISTORY_ID='your_history_id').

To initialize using environment variables: gx_init(API_KEY=Sys.getenv("GX_API_KEY"), GALAXY_URL=Sys.getenv("GX_GALAXY_URL"), HISTORY_ID=Sys.getenv("GX_HISTORY_ID"))

Usage

You can now run gx_list_histories() to list all of your Galaxy histories. Pick a history and set this as your current (default is latest) history by running gx_switch_history('HISTORY_ID').

With gx_get(1) you get the first dataset from your Galaxy history. On completion gx_get(1) shows you where it has been downloaded.

gx_get() also works with collections. It calls gx_get_collection().

By running gx_put(/tmp/some_file.txt) you will upload a file into the current Galaxy history.

gx_list_history_datasets() to get information on every dataset from the history.

Other functions you can discover from the man pages, all functions are prefixed with gx_

Admin

For now this package uses environment variables for the settings, so you can set a default Galaxy instance, e.g. to your local instance. To set the defaults set the same keys as above in e.g. the RStudio's configuration /etc/rstudio/rsession-profile.

Credits

This is based on the work by Helena Rasche and Bjoern Gruening - see the fork origin: https://github.com/erasche/docker-rstudio-notebook

Merged forks from Justin Band, Adrian Zetner and others - please see the commit history.