example_arnie_file.txt

# paths to local installations of packages.  If package is not installed, leave as None
# Replace paths below with paths to your installations.
# NB: .gitignore file ignores *.arnie files. Name it as such if you don't want your local path file 
# included with your git repo.

rnastructure: /path/to/RNAstructure/exe
rnasoft: /path/to/MultiRNAFold
contrafold_2: /path/to/contrafold-se/src
eternafold: /path/to/eternafold/src/
vfold: /path/to/Vfold2D
nupack: /path/to/nupack3.2.2/build/bin

# for a Mac installed binary:
vienna_2: /usr/local/bin
# for path to a vienna build:
vienna_2: /path/to/ViennaRNA-2.4.10/src/bin
vienna_1: /path/to/ViennaRNA-1.8.5/bin

# for linear partition
linearfold: /path/to/LinearFold/bin
linearpartition: /path/to/LinearPartition/bin

# for PK predictors
hotknots: /path/to/HotKnots_v2.0/bin
ipknot: /path/to/ipknot/build
knotty: /path/to/Knotty
pknots: /path/to/PKNOTS/bin
spotrna: /path/to/SPOT-RNA
spotrna_conda_env: /path/to/miniconda3/envs/spotrna/bin
spotrna2: /path/to/SPOT-RNA2
e2efold: /path/to/e2efold/e2efold_productive
e2efold_conda_env: /path/to/miniconda3/envs/e2efold/bin

#TMP: location for tmp files for packages. Update to where you want your tmp files stored.
TMP: /tmp