Content of review 1, reviewed on September 29, 2016
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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Apurva, N., Richard, B., Rob, D., Barun, M., Sergios-Orestis, K., Barry, K., J., P. P. 2016. Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets. GigaScience.