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FROM debian:8.6

LABEL author="Maxime Garcia" \
description="HTSlib 1.4 image for use in CAW" \
maintainer="maxime.garcia@scilifelab.se"
# Dockefile for mosdepth is based on Dockerfile for HTSlib 1.4 by Maxime Garcia
# I just added few lines for quick building a docker image for mosdepth

# Install libraries
RUN apt-get update && apt-get install -y --no-install-recommends \
build-essential \
ca-certificates \
curl \
libbz2-dev \
liblzma-dev \
libncurses5-dev \
libncursesw5-dev \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*

# Setup ENV variables
ENV HTSLIB_BIN="htslib-1.5.tar.bz2" \
HTSLIB_VERSION="1.5" \
MOS_VERSION="v0.1.6" \
LD_LIBRARY_PATH="/usr/local/lib"

# Install HTSlib
RUN curl -fsSL https://github.com/samtools/htslib/releases/download/$HTSLIB_VERSION/$HTSLIB_BIN -o /opt/$HTSLIB_BIN \
&& tar xvjf /opt/$HTSLIB_BIN -C /opt/ \
&& cd /opt/htslib-$HTSLIB_VERSION \
&& make \
&& make install \
&& rm -rf /opt/$HTSLIB_BIN /opt/htslib-$HTSLIB_VERSION \
&& curl -fsSL https://github.com/brentp/mosdepth/releases/download/$MOS_VERSION/mosdepth -o /usr/bin/mosdepth \
&& chmod +x /usr/bin/mosdepth

WORKDIR /data

ENTRYPOINT ["mosdepth"]