Scaffold Batch Annotated XML Driver (SCAFML)
The following XML driver file includes references to the batch processing version of Scaffold for most elements and attributes.
The default values are those used in Scaffold Desktop UI. Interact with
the XML sections to add or remove attributes and build your SCAFML. Use
the copy buttons to paste into a text editor for review. Finally, save
this file with the extension *.scafml.
Command Line Options
To view command line interface options built into the Scaffold Batch
command, run it without arguments:
user@host:~$ ./ScaffoldBatch
ScaffoldBatch [-q] [-f] [-keypath PATH] [xmlDriverFile1] [xmlDriverFile2]
Options:
-h, -help, --help
Shows help documentation
-q, -quiet, --quiet
Write minimal information to console
-f, -force, --force
Doesn't request answers from user
-k, -keypath, --keypath PATH
Specifies location of the license key path -- useful for grid systems.
--is-license-valid-at PATH
Checks if license is valid at the given path
You can also get help information by running with the help option:
user@host:~$ ./ScaffoldBatch --help
Syntax Conventions
Please note that for consistency, Unix-style forward slashes for path designations, and bash-style command syntax will be used throughout this document.
Interactive XML Driver
All SCAFML files start with a pair of Scaffold and
Experiment elements that bracket the rest of the
specification. It is common to add the Scaffold version
attribute here.
Click the buttons and XML sections for more information.
Core Facilities
Managing a core facility or shared resource department? Need help with gaps in your software pipeline? Want to try new methods like DIA proteomics? Do you need an easy way to share results with your customers?
Researchers
Need an elegant yet easy to use solution for data processing? Not sure where to begin when starting up a new lab. Let us help take the pressure off setting up a software pipeline so you can focus on the science.
Tutorials & Videos
Check out our YouTube channel for Scaffold tutorials, from getting started to advanced use. We have videos for all our Scaffold products, as well as videos from previous conferences and special events.
