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UrJTAG aims to create an enhanced, modern tool for communicating over JTAG with flash chips, CPUs, and many more. It is a descendant of the popular openwince JTAG tools with a lot of additional features and enhancements.
This (Python) tool allows you to easily create FPGA bitfiles for your embedded system, from several Open Source IPs (compatibles with the OpenCores Wishbone bus) . It will also generates the corresponding drivers (currently only Linux ones).
ArchC is an open-source architecture description language based on SystemC. Its goal is to provide designers with a tool to evaluate new ideas in processor and ISA design, memory hierarchy, etc. and other aspects of computer architecture research.
FpgaC compiles a subset of the C language to net lists which can be imported into an FPGA vendors tool chains. C provides an excellent alternative to VHDL/Verilog for algorithmic expression of FPGA reconfigurable computing tasks. More info in wiki.
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Parallel Port Eprom Programmer contains a GNU/Linux driver that
controls the eprom programmer throught the parallel port and a tool
which allows reading and writing eproms.