biocondaを使用してCheckMをインストールする

1.bioconda py 27という仮想環境を構築しcheckmをインストール

conda create -n py27 python=2.7 anaconda checkm-genome

conda activate py27

cd ~/
mkdir checkm
cd checkm

curl -L -O curl -L -O https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz

tar xzf checkm_data_2015_01_16.tar.gz 

2.checkmデータベースの設定

checkm data setRoot

(note instructions here are incorrect - you can't specify the path on the command line.)
To analyze, put your genome(s) in .fa files in a directory bins/ under your cwd, and then run:

checkm lineage_wf -x fa --reduced_tree bins out

You can regenerate various reports like so:

checkm qa out/lineage.ms out -f checkm.out.txt