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Dockerfile
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FROM openjdk:8
LABEL authors="[email protected],[email protected]" \
description="Docker image containing all requirements for NGI-MethylSeq pipeline"
# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
RUN apt-get update && \
apt-get install -y --no-install-recommends \
g++ \
gcc \
gfortran \
libbz2-dev \
libcurl4-openssl-dev \
libgsl0-dev \
liblzma-dev \
libncurses5-dev \
libpcre3-dev \
libreadline-dev \
libssl-dev \
make \
python-dev \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*
# Install pip
RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \
python /opt/get-pip.py && \
rm /opt/get-pip.py
RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -o /opt/fastqc_v0.11.5.zip && \
unzip /opt/fastqc_v0.11.5.zip -d /opt/ && \
chmod 755 /opt/FastQC/fastqc && \
ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
rm /opt/fastqc_v0.11.5.zip
# Install cutadapt
RUN pip install cutadapt
# Install TrimGalore
RUN mkdir /opt/TrimGalore && \
curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v0.4.2.zip -o /opt/TrimGalore/trim_galore_v0.4.2.zip && \
unzip /opt/TrimGalore/trim_galore_v0.4.2.zip -d /opt/TrimGalore && \
ln -s /opt/TrimGalore/trim_galore /usr/local/bin/trim_galore && \
rm /opt/TrimGalore/trim_galore_v0.4.2.zip
# Install SAMTools
RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 -o /opt/samtools-1.3.1.tar.bz2 && \
tar xvjf /opt/samtools-1.3.1.tar.bz2 -C /opt/ && \
cd /opt/samtools-1.3.1 && \
make && \
make install && \
rm /opt/samtools-1.3.1.tar.bz2
# Install PicardTools
RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/picard-tools-2.0.1.zip -o /opt/picard-tools-2.0.1.zip && \
unzip /opt/picard-tools-2.0.1.zip -d /opt/ && \
rm /opt/picard-tools-2.0.1.zip
ENV PICARD_HOME /opt/picard-tools-2.0.1
# Install Bismark
RUN mkdir /opt/Bismark && \
curl -fsSL https://github.com/FelixKrueger/Bismark/archive/0.17.0.zip -o /opt/Bismark/bismark.zip && \
unzip /opt/Bismark/bismark.zip -d /opt/Bismark && \
ln -s /opt/Bismark/Bismark-0.17.0/bam2nuc /usr/local/bin/bam2nuc && \
ln -s /opt/Bismark/Bismark-0.17.0/bismark /usr/local/bin/bismark && \
ln -s /opt/Bismark/Bismark-0.17.0/bismark2bedGraph /usr/local/bin/bismark2bedGraph && \
ln -s /opt/Bismark/Bismark-0.17.0/bismark2report /usr/local/bin/bismark2report && \
ln -s /opt/Bismark/Bismark-0.17.0/bismark2summary /usr/local/bin/bismark2summary && \
ln -s /opt/Bismark/Bismark-0.17.0/bismark_genome_preparation /usr/local/bin/bismark_genome_preparation && \
ln -s /opt/Bismark/Bismark-0.17.0/bismark_methylation_extractor /usr/local/bin/bismark_methylation_extractor && \
ln -s /opt/Bismark/Bismark-0.17.0/coverage2cytosine /usr/local/bin/coverage2cytosine && \
ln -s /opt/Bismark/Bismark-0.17.0/deduplicate_bismark /usr/local/bin/deduplicate_bismark && \
ln -s /opt/Bismark/Bismark-0.17.0/filter_non_conversion /usr/local/bin/filter_non_conversion && \
rm /opt/Bismark/bismark.zip
# Install Qualimap
RUN mkdir /opt/Qualimap && \
curl -fsSL https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip -o /opt/Qualimap/qualimap.zip && \
unzip /opt/Qualimap/qualimap.zip -d /opt/Qualimap && \
ln -s /opt/Qualimap/qualimap_v2.2.1/qualimap /usr/local/bin/qualimap && \
rm /opt/Qualimap/qualimap.zip
# Install BWA
RUN mkdir /opt/bwa && \
curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.15.tar.bz2 -o /opt/bwa/bwa.tar.bz2 && \
tar xvjf /opt/bwa/bwa.tar.bz2 -C /opt/bwa/ && \
cd /opt/bwa/bwa-0.7.15/ && \
make && \
ln -s /opt/bwa/bwa-0.7.15/bwa /usr/local/bin/bwa && \
rm /opt/bwa/bwa.tar.bz2
# Install bwa-meth
RUN pip install toolshed && \
pip install git+git://github.com/brentp/bwa-meth.git
# Install MethylDackel
RUN mkdir /opt/MethylDackel && \
curl -fsSL https://github.com/dpryan79/MethylDackel/archive/0.2.1.zip -o /opt/MethylDackel/MethylDackel.zip && \
unzip /opt/MethylDackel/MethylDackel.zip -d /opt/MethylDackel && \
cd /opt/MethylDackel/MethylDackel-0.2.1 && \
make && \
make install prefix=/usr/local/bin && \
rm /opt/MethylDackel/MethylDackel.zip
# Install MultiQC
RUN pip install git+git://github.com/ewels/MultiQC.git