dtools

Multitude of rna structure programs made to run through docker (No Setup Required)

Prerequisites

Make sure you have docker installed. We provide an installation script for ubuntu 20.04. You will have to run it with elevated privileges (not as root) sudo ./install_docker.sh

Important

Always use the files folder to pass files to and from programs.

DinoKnot

Install by running ./Dinoknot/install.sh

Run the program (remember to pass arguments) ./Dinoknot/run.sh

Example usage ./Dinoknot/run.sh -i files/dinoknot_example.txt --t1 RNA --t2 DNA -o files/outputfile.txt

HFold

Install by running ./Hfold/install.sh

Run the program (remember to pass arguments) ./Hfold/run.sh

Example usage ./Hfold/run.sh --i files/hfold_example.txt --o files/outputfile.txt

Iterative HFold

Install by running ./Iterative-Hfold/install.sh

Run the program (remember to pass arguments) ./Iterative-Hfold/run.sh

Example usage ./Iterative-Hfold/run.sh --i files/iterative-hfold_example.txt --o files/outputfile.txt

Knotty

Install by running ./Knotty/install.sh

Run the program (remember to pass arguments) ./Knotty/run.sh

Example usage ./Knotty/run.sh GCAACGAUGACAUACAUCGCUAGUCGACGC > files/outputfile.txt

IPknot

Install by running ./Ipknot/install.sh

Run the program (remember to pass arguments) ./Ipknot/run.sh

Example usage ./Ipknot/run.sh files/ipknot_example.txt > files/outputfile.txt

HotKnots

Install by running ./Hotknots/install.sh

Run the program (remember to pass arguments) ./Hotknots/run.sh

Example usage ./Hotknots/run.sh -I files/hotknots_example > files/outputfile.txt

SPOT-RNA

Install by running ./Spot-Rna/install.sh

Run the program (remember to pass arguments) ./Spot-Rna/run.sh

Example usage ./Spot-Rna/run.sh --inputs files/spotrna_example.txt --outputs 'files/' --cpu 32

ivanpmartell/dtools