env-metagenomics-analysis

Creating requirement file to reproduce the analysis:

conda list > requirements.txt # this file has info of all installed packages.
conda env export --no-builds > environment.yml # use this file to recreate exact same conda env.
conda activate mg # mg for metagenomics

Installing tools in dedicated conda environment:

conda env list
conda create -n mg -y # mg for metagenomics
conda activate mg

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda install -y fastqc=0.11.9 trimmomatic=0.39 kraken2=2.1.2 krona=2.8.1 maxbin2=2.2.7 spades=3.15.2 kraken-biom=1.2.0 checkm-genome=1.2.1

# checking installation:
which run_MaxBin.pl # for maxbin
which spades
which ktImportText # for krona
which checkm
which kraken-biom

Additional Setup:

bash ~/anaconda3/envs/mg/opt/krona/updateTaxonomy.sh 
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
tar -xzf taxdump.tar.gz
mkdir -p .taxonkit/
cp names.dmp nodes.dmp delnodes.dmp merged.dmp .taxonkit
rm *dmp readme.txt taxdump.tar.gz gc.prt