linsalrob/cami-focus repository overview

This is Rob's installation of FOCUS⁠ for the CAMI Challenge⁠.

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.