BootStrap: docker From: continuumio/miniconda:latest IncludeCmd: yes %post # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # this will install all necessary packages and prepare the container apt-get -y update apt-get -y install make gcc zlib1g-dev libncurses5-dev wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 \ && tar -xjf samtools-1.3.1.tar.bz2 \ && cd samtools-1.3.1 \ && make \ && make prefix=/usr/local install export PATH=/opt/conda/bin:$PATH conda install --yes -c bioconda \ star=2.5.2b \ sailfish=0.10.1 \ fastqc=0.11.5 \ kallisto=0.43.0 \ subread=1.5.0.post3 conda clean --index-cache --tarballs --packages --yes mkdir /gpfs /spin1 /gs2 /gs3 /gs4 /gs5 /gs6 /data /scratch /fdb /lscratch cat > /singularity <<'EORUNSCRIPT' #!/bin/bash # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # this text will get copied to /singularity and will run whenever the container # is called as an executable function usage() { cat <