For this service, which offers both a command-line interface, Python library or interactive user interface, that means developers get the option to choose between different Nvidia GPUs, for example.
The BioPAX Validator is a command-line tool, Java library and online web service for BioPAX that performs >100 classes of consistency checks.
The code uses the Boost library for command-line argument processing, advanced file operations and REgular EXpression (regex) parsing.
The chemfp package is a set of command-line tools and a Python library for fingerprint generation and high-speed Tanimoto search.
Six open source Java software systems were selected for the study: (1) ANTa: is a Java library and command-line tool that drives processes described in build files as targets and extension points dependent upon each other.
Command-line based alternatives and imaging libraries also exist, which require users to prepare all data and customisation through text files, such as Circos [ 15], CGView [ 16], Genome Diagram [ 17] and BLASTAtlas [ 18].
The WiggleTools library can be used as a C library but also as a standalone command-line tool.
The access via the API or the binary using the command-line interface enables the user to utilize the library for batch processing.
The SMILES of the designed RECAP library were standardized using the ChemAxon Command-Line Standardizer where the following options were selected: "Remove Fragment" (keep largest), "Neutralize", "RemoveExplicitH", "Clean2D", "Mesomerize" and "Tautomerize" [56].
The software provides an API for use as a library, and also has both a command-line user interface and a graphical user interface for interactive high level use as a standalone application.
For example, the following command creates a bedGraph file of read coverage for the hg19 assembly: The pybedtools package provides a convenient and flexible interface to both the BEDTools command-line tools and efficient functions in the BEDTools C++ libraries.
