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. |
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. |