Awesome

Clone

• Download & install git-lfs

• Initialize git-lfs

  git lfs install
  

• Clone

  git clone $repo $dir; cd $dir
  

Eclipse

Import

• File > Open Projects from File System...
• Directory...
• $dir (where you cloned the repository)
• Window > Preferences > Java > Build Path > User Libraries
• Import > Browse... > $dir/Cello/Cello.userlibraries
• Ok > Apply & Close

Build

• Navigate to Cello project
• Navigate to build.xml, right-click, Run As > Ant Build
• Right-click on Cello project, Refresh

Run/Debug configuration

• Run > Run Configurations...

• Java Application (right click) > New

• Main tab

  • Project: Cello
  • Main class: DNACompiler.runtime.Main

• Arguments tab

  • Program arguments:

    -inputNetlist "${project_loc}/sample-input/DNACompiler/adder/adder.v"
    -targetDataFile "${project_loc}/sample-input/DNACompiler/adder/Eco1C1G1T1.UCF.json"
    -options "${project_loc}/sample-input/DNACompiler/adder/options.csv"
    -netlistConstraintFile "${project_loc}/sample-input/DNACompiler/adder/adder_netlistconstraints.json"
    -outputDir "${project_loc}/sample-output/adder"
    

• Environment tab

  • New...

  • Name: LD_LIBRARY_PATH

  • Value:

    ${project_loc}/src/resources-partitioning/algorithms/GPCC_SCIP/linux64:${project_loc}/src/resources-partitioning/algorithms/GPCC_SUGARM_BASE/linux64
    

• Apply

• May need to invoke the Ant build script once, then right click on the project, Refresh

Command line

Build

cd $dir
ant

Test DNACompiler application

cd $dir/exec
./run.py -e DNACompiler -j "-Xms2G -Xmx5G" -a " \
-inputNetlist ../sample-input/DNACompiler/rule30/rule30.v \
-targetDataFile ../sample-input/DNACompiler/rule30/Eco1C1G1T1-synbiohub.UCF.json \
-options ../sample-input/DNACompiler/rule30/options.csv \
-outputDir /path/to/outputdir"

Test export stage

cd $dir/exec
./run.py -e export -j "-Xms2G -Xmx5G" -a " \
-inputNetlist ../sample-input/export/placement.json \
-targetDataFile ../sample-input/export/Eco1C1G1T0-synbiohub.UCF.json \
-options ../sample-input/export/options.csv \
-outputDir /path/to/outputdir \
-algoName SBOL"