Open Source Linux Command Line Tools

Arduino CLI is an all-in-one solution that provides Boards/Library Managers, sketch builders, board detection, uploader, and many other tools needed to use any Arduino compatible board and platform from the command line or machine interfaces. In addition to being a standalone tool, Arduino CLI is the heart of all official Arduino development software (Arduino IDE, Arduino Web Editor). The script requires sh, which is always available on Linux and macOS. sh is not available by default on Windows, though it is available as part of Git for Windows (Git Bash). If you don't have sh available, use the "Download" installation option. If you would like to use the arduino-cli command from any location, install Arduino CLI to a directory already in your PATH or add the Arduino CLI installation path to your PATH environment variable.

The project development has been moved on GitHub https://github.com/pcb2gcode/pcb2gcode The GUI for pcb2gcode can be found here https://github.com/pcb2gcode/pcb2gcodeGUI pcb2gcode is a command-line tool for isolation, routing and drilling of PCBs that provides full support for both single- and double-sided boards. For more information, see http://sourceforge.net/apps/mediawiki/pcb2gcode/

C3D is a command-line tool for converting 3D images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling.

Simple command-line tool to download/upload firmware to/from STM32 MCU with factory preprogrammed serial bootloader. Look <a href="http://openfacts2.berlios.de/wikien/index.php/BerliosProject:STM%20Flasher">wiki</a> for more info.

The ultimative shared library to do calculations(!) and conversions with any units! Includes all SI and pseudo SI units and thousands of US, Imperial and other units. 10th of thousands of typical dimensions are recognised as well. An easy API for calculations is available as well as a ncurses based calculator providing RPN and algebraic mode.

ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract

A command line tool that allows a semi-automated scientific articles management. It assumes an existence of a directory of a specific format in the file system. The tool interprets the data stored in the directory (called a repository), extend it via the usage of some automatic tools such as pdftotext, and search the text as well as some metadata.

If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).

CSV Comparator is a tool for comparing files which contain CSV-Data. It was created for performance engineers to be able to have a easy way to compare data from two testruns and be able to automate the comparing process of various files with scripts. There is a command line tool as well as a user interface. In case you need to compare .xml-Files you can convert them to .csv-Files with my other project CSV Transformer. The advantages by using CSV as input and output are the following: - Many applications allow an export of its data to CSV or Excel(were it could be saved to CSV) - It is possible to pre- and postprocess the data, e.g removing version numbers before comparing - It is easy to create CSV data from logfiles and other resources by using unix tools like sed or awk - CSV can be loaded into other applications, especially Excel, were it can be formatted by macros for analyzing.

Command line tool to generate Gcode for CNC applications from DXF files. Originally written for 2-axis machines such as foam cutters, it now supports 3-axis machines.

An implementation of Dantzig-Wolfe decomposition built upon the GNU Linear Programming Kit. This is a command line tool for solving properly decomposed linear programs. There are several examples and some documentation to guide the use of this solver. Forked over to GitHub (see link).

Elastolix takes any 2 of 6 elastic moduli and calculates the remaining 4. There is a command line tool, named elastolix and a tool with a graphical user interface made with lazarus. Releases for macOS will always be first, others should always follow shortly after.

FREJ stands for "Fuzzy Regular Expressions for Java" - it is a command-line tool and library which allow you easily compare strings with patterns disregarding nasty typos and considering several variants (like "Barack Obama", "B.H.Obama" etc.) Project sources are moved to github: https://github.com/RodionGork/FREJ

Gebabbel is a GUI for the famous gpsbabel, a command line tool to convert various GPS file formats back and forth. Thanks to gpsbabel, you cannot only convert files but also exchange data with your GPS device (e.g. Garmin and Magellan) directly.

Input 1 - A training dataset (multiple observations) of up to four variables (predictors) against one (response variable) Input 2 - A test dataset (multiple observations) of the same four variables with unknown response variable Output - Calculation of the response variable for each test observation using fuzzy logic or fuzzy rule-based Bayesian algorithms HABFUZZ is a habitat model, which can be used in ecohydraulic modelling applications for the calculation of the instream habitat suitability in various discharge scenarios in a simulated river reach. It comes with no graphical user interface but it's a one-click tool. Just provide your input and let HABFUZZ provide you the output. The HABFUZZ manual https://github.com/chtheodoro/habfuzz/blob/master/HABFUZZ_v2.5_manual.pdf HABFUZZ in the Journal of Open Source Software http://joss.theoj.org/papers/1ad27db8f0976c28a75e20d34eba5ee2 HABFUZZ website https://chtheodoro.wixsite.com/habfuzz

A command-line tool for numerical reconstruction of digital holograms (formerly known as "HoloPlay")

IMG2GSLIB is a small command line tool that converts images to grids into GEO-EAS format readable by geoscientific software such as GSLIB, SGeMS, Isatis, Gocad, Petrel, etc. It now can output 3D volumes from image stacking. The ASCII result is sent to stdout, so you can redirect it using the > operator if you want to save it to a file. Run java -jar IMG2GSLIB.jar without arguments to get help on usage. Requirements: -Java 1.7

At the moment its simple command line tool to create nice looking schematic libraries in kicad. I hope that it would be usefull for someone. dont need to click anything just write/paste pin names and thats it.

This is a small and fast library and command-line tool for manipulation of logic/boolean-algebra expressions, including proofing and simplification. A front-end using tigcc for Texas Instruments calculators is planned, too.

This is a Python interface for reading and writing Magellan GPS unit map files. There is also a command line tool for creating GPS maps from OpenStreetMap data.

Mesh2HRTF is an open-source project aiming at providing an easy-to-use software package for the numerical calculation of HRTFs. It targets researchers in the field of binaural audio. In a nutshell, Mesh2HRTF simply reads geometrical data, calculates the corresponding sound field and outputs HRTFs. To support multiple computer platforms, the concept of Mesh2HRTF is to focus on a command-line tool, which forms the numerical core, i.e., an implementation of the 3-dimensional Burton-Miller collocation BEM coupled with the multi-level fast multipole method (ML-FMM), and to provide add-ons for existing cross-platform applications for the preprocessing of geometrical data and for the visualization of results.

This project implements in C++ a bunch of known Neural Networks. So far the project implements: LVQ in several variants, SOM in several variants, Hopfield network and Perceptron. Other neural network types are planned, but not implemented yet. The project can run in two modes: command line tool and Python 7.2 extension. Currently, Python version appears more functional, as it allows easy interaction with algorithms developed by other people.

A very simple command line tool to convert OSM files to Shapefiles. Written in Java. Think of it as a self-study project.

PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be concurrently used to generate cleavage specificity visualizations like the iceLogo (https://iomics.ugent.be/icelogoserver/create).

IMPORTANT NOTE: This project has been migrated to GitHub and is no longer maintained here. Please refer to: https://github.com/suhrig/pingpongpro Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs, predominantly active in the germ line. There, they limit the detrimental effect of transposons on the genome. They do so by forming a complex with Piwi proteins. The complex binds and then cleaves mRNA molecules of active transposons. The resulting mRNA fragments induce the production of more piRNAs, thus reinforcing the anti-transposon response in a feed-forward loop called the "ping-pong cycle". A key question in ping-pong cycle research is identification of piRNAs which are amplified through the cycle. PingPongPro is a command-line tool for detecting ping-pong cycle activity in piRNA-Seq data. PingPongPro was developed at the Institute of Molecular Biology gGmbH in Mainz.