Build docker image

docker build -t picrust2-image .

Run and mount data

docker run -it -v /data:/data picrust2-image

Inside container example

source activate picrust2

place_seqs.py -t sepp -s ./seqs.fna --ref_dir oldIMG -o out.tre -p 1 --intermediate intermediate/place_seqs

hsp.py -db oldIMG -i 16S -t out.tre -o marker_predicted_and_nsti.tsv.gz -p 1 -n

hsp.py -db oldIMG -i EC -t out.tre -o EC_predicted.tsv.gz -p 1

metagenome_pipeline.py -i table.biom -m marker_predicted_and_nsti.tsv.gz -f EC_predicted.tsv.gz -o EC_metagenome_out --strat_out