Three commands to start analysing your metagenome data:
conda install -c bioconda -c conda-forge metagenome-atlas
atlas init --db-dir databases path/to/fastq/files
atlas run
All databases and dependencies are installed on the fly in the directory db-dir.
You want to run these three commands on the example_data on the GitHub repo.
If you have more time, then we recommend you configure atlas according to your needs.
- check the
samples.tsv - edit the
config.yaml - run atlas on any cluster system For more details see documentation.
Atlas is a easy to use metagenomic pipeline
Atlas is still under active development; therefore, you may want to install the up to date atlas from GitHub. Atlas should be run on linux, the assembly works also on OS X, but unfortunately not the tools used for binning.
Create a conda environment with all primary dependencies. All further dependencies are installed on the fly.
conda create -n atlas -c bioconda -c conda-forge python=3.6 snakemake pandas bbmap=37.78 click=7 ruamel.yaml biopython
Load the environment:
source activate atlas
copy code from GitHub and install:
git clone https://github.com/metagenome-atlas/atlas.git
cd atlas
pip install --editable .
Now you should be able to run atlas:
atlas init --db-dir databases path/to/fastq/files
atlas run
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