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Table 1 A summary of commands available in the latest development version of the repo package

From: repo: an R package for data-centered management of bioinformatic pipelines

Command Description
attach Store a generic file into the repository.
attr Retrieves item attributes.
build Runs code chunk associated with an item and dependant items if needed.
bulkedit Saves repository meta data to a text file for offline editing or loads the file after editing.
check Checks MD5-consistency of stored items.
chunk Displays the code chunk associated with an item.
copy Copies items between repositories.
cpanel Runs visual interface.
dependencies Returns and/or plots item dependencies.
export Saves the contents of a repository item to a file in RDS format.
find Searches all metadata for a partial string match.
get Loads an item into the current workspace.
handlers Returns a list of functions to be used as an alternative interface to the repository.
has Checks wether an item is present in the repository.
info Displays a summary of information about a regular item, a project item, or the repository.
lazydo Evaluates specified code caching results in the repository. Loads results if already cached.
options Sets default parameters to be used by subsequent calls to the put command.
pies Shows statistics about disk space used by each item in the repository.
print Summarizes information about items.
project Creates a special “project” item.
pull Overwrites item contents by downloading data from the associated URL.
put Stores new data into the repository.
related Lists items related to a given item according to dependencies.
rm Removes items from the repository.
root Returns repository root position on the file system.
set Updates an existing item.
stash Stores an item with unspecified meta information.
stashclear Removes stash-ed items.
sys Runs a system command on a given item.
tag Set tags for an item.
tags Retrieves tags for an item.
untag Removes specified tags from an item.
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