Dockerfile.multi

FROM ghcr.io/martinluttap/bio-ubuntu:1.0.0 AS builder

ARG VERSION

ENV URL=http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${VERSION}.zip

RUN apt-get update \
	&& apt-get install -y \
		build-essential \
		libfontconfig1 \
		openjdk-11-jre-headless \
		perl-modules \
		wget \
		unzip \
	&& apt-get clean \
	&& rm -rf /var/lib/apt/lists/*

# Example download and compile step
ADD $URL /usr/local/bin
RUN cd /usr/local/bin \
	&& unzip fastqc_v${VERSION}.zip \
	&& rm -rf fastqc_v${VERSION}.zip \
	&& sed -i 's/kmer[[:space:]]\+ignore[[:space:]]\+1/kmer ignore 0/' $PWD/FastQC/Configuration/limits.txt \
	&& sed -i 's/assistive_technologies/#assistive_technologies/' /etc/java-11-openjdk/accessibility.properties \
	&& chmod 755 FastQC/fastqc \
	&& ln -s $PWD/FastQC/fastqc /usr/local/bin/fastqc

# ENTRYPOINT ["/usr/local/bin/fastqc"]