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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
%runscript
#!/bin/bash
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# this text will will run whenever the container is called as an executable
function usage() {
cat <<EOF
NAME
rnaseq - rnaseq pipeline tools 0.1
SYNOPSIS
rnaseq tool [tool options]
rnaseq list
rnaseq help
DESCRIPTION
Singularity container with tools to build rnaseq pipeline.
EOF
}
function tools() {
echo "conda: $(which conda)"
echo "---------------------------------------------------------------"
conda list
echo "---------------------------------------------------------------"
echo "samtools: $(samtools --version | head -n1)"
}
arg="${1:-none}"
case "$arg" in
none) usage; exit 1;;
help) usage; exit 0;;
list) tools; exit 0;;
# just try to execute it then
*) $@;;
esac
%environment
export PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda
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