Public Repository

Last pushed: 3 years ago
Short Description
An installation of focus for the CAMI challenge
Full Description

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 


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.

Docker Pull Command