Singularity

Bootstrap: docker
From: ubuntu:20.04
IncludeCmd: yes

%environment
#R_VERSION=4.1
#export R_VERSION
#R_CONFIG_DIR=/etc/R/
#export R_CONFIG_DIR
export LC_ALL=C
export PATH=$PATH:/opt/software/miniconda3/bin:/opt/software/mOTUs:/opt/software/read_counter

%post
  apt-get update
  apt-get install -y apt-transport-https apt-utils software-properties-common
  apt-get install -y add-apt-key
  export DEBIAN_FRONTEND=noninteractive
  ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime
  apt-get install -y tzdata
  dpkg-reconfigure --frontend noninteractive tzdata

  apt-get install -y wget python3-pip git

  mkdir -p /opt/software

  wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 
  bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/software/miniconda3
  rm -f Miniconda3-latest-Linux-x86_64.sh

  /opt/software/miniconda3/bin/conda install -y -c conda-forge -c bioconda hmmer 'samtools>=1.13' bwa kraken2 'gatk4==4.1.6.0-0' fastqc multiqc bbmap seqtk