README_example_cmds.md

• Install MarkerMAG on Katana with Python virtual environment

  module load python/3.7.3
  mkdir ~/mypython3env_MarkerMAG
  python3 -m venv --system-site-packages ~/mypython3env_MarkerMAG
  source ~/mypython3env_MarkerMAG/bin/activate
   
  # install with 
  pip3 install MarkerMAG
    
  # upgrade with 
  pip3 install --upgrade MarkerMAG
  

• To run MarkerMAG, just run the following commands to activate python's virtual environment and load needed modules.

  module load python/3.7.3
  source ~/mypython3env_MarkerMAG/bin/activate
  module load R/4.0.2
  module load blast+/2.11.0
  module load bowtie/2.3.5.1
  module load samtools/1.10
  module load spades/3.14.0
  module load gcc/8.4.0
  module load boost/1.73.0-gcc8   
  module load java/8u201-jdk
  module load bbmap/38.51
  module load seqtk/20190219
  module load mafft/7.407
  module load perl/5.28.0
  module load hmmer/3.2.1
  module load bedtools/2.27.1
  module load barrnap/0.9
  module load usearch/11.0.667
  cd /srv/scratch/zID
  MarkerMAG link -p Soil -marker Soil_16S.fa -mag Soil_MAGs -x fa -r1 R1.fa -r2 R2.fa -t 12