iamvazu / cello2

Cello2 is the continuation of the Cello genetic circuit design software.

Requirements

• Java JDK 8 (Oracle, OpenJDK)
• Python 3
• Maven
• Yosys
  • Linux: check your package manager
  • Mac OSX: brew install yosys
  • Windows:
    • download yosys-win32-mxebin-0.8.zip here: http://www.clifford.at/yosys/download.html
    • unzip anywhere, add the folder containing yosys.exe to %Path%
• Graphviz
  • Linux: check your package manager
  • Mac OSX: brew install graphviz
  • Windows:
    • download and install latest msi, e.g. graphviz-2.38.msi
    • add path to dot.exe, e.g. C:\Program Files (x86)\Graphvix2.38\bin, to %Path%

Installation

Manual

Clone the repository.

git clone https://github.com/CIDARLAB/Cello2.git

Build.

cd Cello2/cello2
mvn clean install

Test.

cd target
./run.py -e DNACompiler -j "-Xms2G -Xmx5G" -a " \
-targetDataFile ../../sample-input/DNACompiler/and/Eco1C1G1T1-synbiohub.UCF.json \
-inputNetlist ../../sample-input/DNACompiler/and/and.v \
-options ../../sample-input/DNACompiler/and/options.csv \
-outputDir /path/to/output/dir