Bootstrap: docker
From: ubuntu:18.04

%labels
MAINTAINER Laurent Modolo

%post
mkdir -p /sps /pbs /scratch
KALLISTO_VERSION=0.43.1
PACKAGES="curl \
ca-certificates"

apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean

curl -k -L  https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
rm -Rf kallisto_linux-v${KALLISTO_VERSION}*

%environment
export KALLISTO_VERSION=0.44.0

%runscript
exec /bin/bash "$@"