Review for "Clusterflock: A Flocking Algorithm for Isolating Congruent Phylogenomic Datasets"

Completed on 29 Sep 2016 by Peter Li.

License: http://creativecommons.org/licenses/by/4.0/

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Comments to author

Reviewer #1 reported problems with using the Clusterflock tool due to the complexity with installing the software and its dependencies. In response, the authors of Clusterflock have provided a Docker container which ships all of the code and associated software libraries in a standalone package ready for use.

I have tested the clusterflock-0.1 Docker container and can report that I have successfully executed the clusterflock.pl and clusterflock_simulations.pl scripts to completion using the instructions available from https://github.com/narechan/clusterflock/blob/master/MANUAL. This involved:

1. Deploying an Ubuntu-14.04 EC2 virtual server as a t2.medium instance on the AWS cloud and installing the Docker software on it.

2. Downloading the narechan/clusterflock-0.1 Docker image from DockerHub onto the virtual server.

3. The Clusterflock scripts can then be executed by running the clusterflock-0.1 Docker container with this command on the host server: 
$ docker run -v /mount/path/on/host:/home/test -it narechan/clusterflock-0.1

The following two commands can then be executed using clusterflock-0.1 Docker image:

$ clusterflock.pl -i test_data/4/fastas/ -c config.boids.simulations -l test_data/4/4.lds -s all -b 1 -d -x -o /home/test/4_out

$ clusterflock_simulations.pl -c config.boids.simulations -r 10 -p 10 -o /home/test/4_sim/ -i test_data/4/fastas/ -l test_data/4/4.lds -j /home/clusterflock/dependencies/elki-bundle- 0.6.5~20141030.jar -k 4 -f 500 > /home/test/4_sim.avg_jaccard

Both of the above commands generated outputs as described in https://github.com/narechan/clusterflock/blob/master/MANUAL.

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An article whose findings are important to those with closely related research interests

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Acceptable

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