If you have docker installed, you should be able to get this container and run it.
You need to change /path/to/host_dir/ to a real path on your machine, and you need two files, a fastq file and input/fastq.list should have one line per file and list fastq file(s) The location of the file should be as it will appear in the docker, so instead of /path/to/host_dir/input use /dckr/mnt/input
You should create a docker directory and in there put an input and output directory, and cd to the docker directory
mkdir -p docker/input docker/output cd docker
And then put your fastq file and list file in the input dir something like this:
$ ls input output $ ls input/ fastq.list test.fastq.gz $ cat input/fastq.list /dckr/mnt/input/test.fastq.gz $
and then you should be able to pull the docker image with
docker pull linsalrob/cami-focus
and to run the image
docker run -v "$PWD/input/:/dckr/mnt/input:ro" -v "$PWD/output:/dckr/mnt/output:rw" -e "DCKR_THREADS=16" -e "CONT_FASTQ_FILE_LISTING=/dckr/mnt/input/fastq.list" -e "CONT_PROFILING_FILE=/dckr/mnt/output/results.out" --rm linsalrob/cami-focus default
If you do that in output you get a results.out file that is the focus output.
Note that currently the output format is not in CAMI format.