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genome

  • genome storage and analysis unit

introduction

  • mantains some snakemake modules, and can also import python functions to handle the output.

installation

create environment

the main environment is defined here

mamba env create -p .snakemake/conda/snakemake-g -f https://raw.githubusercontent.com/Hocnonsense/genome/master/genome/pyrule/envs/genome.yaml
conda activate .snakemake/conda/snakemake-g
pip install git+https://github.com/Hocnonsense/genome.git

or with a specific version:

version="0.2.3"
mamba env create -p snakemake-g-$version -f https://raw.githubusercontent.com/Hocnonsense/genome/$version/genome/pyrule/envs/genome.yaml
conda activate snakemake-g-$version
pip install git+https://github.com/Hocnonsense/genome.git@$version

some post-deploy settings are defined here

to set database for checkm, you should specific a directory (e.g., ~/.checkm):

export CHECKM_DATA_PATH=~/.checkm
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar -zxvf checkm_data_2015_01_16.tar.gz -C $CHECKM_DATA_PATH
checkm data setRoot $CHECKM_DATA_PATH

update

it is recommanded to create a new conda environment

create other conda environment

from genome.create_conda_env import create_conda_env_gene_clust

create_conda_env_gene_clust()
from genome.create_conda_env import list_envs, create_conda_env

create_conda_env(*list_envs())

compositon

  • snakemake
  • python
  • bash

changelog

tests

# normal tests
python -m pytest -vv --cov --cov-report=html

# also run tests with computation-heavily functions e.g. checkm and binning
python -m pytest -vv --cov --cov-report=html -m "not limit_resource"