Lightweight Reproducible Reporting
Read configuration
Copy files from a packet
Declare a dependency
Describe the current packet
Show an example file
Copy a simple orderly example
Update a gitignore file
Compute a hash
Initialise an orderly repository
Set search options for interactive use
List source reports
Add a new location
Fetch metadata from a location
List known pack locations
Pull one or more packets from a location
Push tree to location
Remove a location
Rename a location
Extract metadata from orderly packets
Read outpack metadata json file
Read outpack metadata
Migrate orderly source code
Create a new report
Declare orderly parameters
Parse the orderly entrypoint script
Add metadata from plugin
Fetch plugin context
Register an orderly plugin
Prune orphan packet metadata
Declare orderly artefacts
Clean up source directory
Compare the metadata and contents of two packets.
Print the details of a packet comparison.
Set configuration options
Explain a query
Construct outpack query
Declare orderly resources
Information about currently running report
Run a report
Packet search options
Query orderly's database
Copy shared resources into a packet directory
Enable orderly strict mode
Validate unpacked packets.
Deprecated functions in orderly. These functions still work (**for now...
Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.