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Changes for 1.3.0 #40

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34 changes: 20 additions & 14 deletions Dockerfile.base
Original file line number Diff line number Diff line change
@@ -1,39 +1,45 @@
# This Dockerfile builds the quatradis base image with all main dependencies which are not
# dependent on any other source code. Using this image as the base provides a big speed up
# when building and testing quatradis.
FROM debian:bullseye-slim
FROM debian:bookworm-slim

# Install the system dependencies
RUN apt-get update -qq && \
apt-get install -y sudo bzip2 curl default-jre gcc gzip locales make procps unzip wget && \
apt-get install -y dirmngr gnupg apt-transport-https ca-certificates software-properties-common && \
apt-get install -y bwa minimap2 smalt
RUN apt-get update -qq

# Install build tools
RUN apt-get install -y sudo bzip2 curl default-jre gcc gzip locales make procps unzip wget dirmngr gnupg apt-transport-https ca-certificates software-properties-common

# Install aligners
RUN apt-get install -y bwa minimap2 smalt

# Setup R
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7' && \
add-apt-repository 'deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/' && \
add-apt-repository 'deb http://cloud.r-project.org/bin/linux/debian bookworm-cran40/' && \
apt-get update -qq && \
apt-get install -y r-base

# Install R dependencies
RUN Rscript -e "install.packages('BiocManager')" -e "BiocManager::install()" -e "BiocManager::install(c('edgeR','getopt', 'MASS'))"

# Install headers for build samtools and htslib
RUN apt-get install -y libcurl4-openssl-dev libdeflate-dev

# Install HTSlib to get bgzip installed as an executable
RUN wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2 -O htslib.tar.bz2 && \
RUN wget https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2 -O htslib.tar.bz2 && \
tar -xjvf htslib.tar.bz2 && \
cd htslib-1.3.2 && \
cd htslib-1.20 && \
make && \
make install && \
rm /htslib.tar.bz2 && rm -r /htslib-1.3.2
rm /htslib.tar.bz2 && rm -r /htslib-1.20

# Install samtools
RUN wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 -O samtools.tar.bz2 && \
RUN wget https://github.com/samtools/samtools/releases/download/1.20/samtools-1.20.tar.bz2 -O samtools.tar.bz2 && \
tar -xjvf samtools.tar.bz2 && \
cd samtools-1.17 && \
cd samtools-1.20 && \
./configure && \
make && \
make install && \
rm /samtools.tar.bz2 && rm -r /samtools-1.17
rm /samtools.tar.bz2 && rm -r /samtools-1.20


# Install snakemake
Expand All @@ -51,7 +57,7 @@ RUN /bin/bash -c "curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-
bash miniconda.sh -b -p /opt/conda && \
rm miniconda.sh"
RUN /bin/bash -c "conda install -y -c conda-forge mamba && \
mamba create -q -y -c conda-forge -c bioconda -n quatradis python=3.10 snakemake snakemake-minimal && \
mamba create -q -y -c conda-forge -c bioconda -n quatradis python=3.11 snakemake snakemake-minimal && \
source activate quatradis && \
mamba install -q -y -c conda-forge -c bioconda snakemake snakemake-minimal && \
mamba install -q -y -c conda-forge singularity && \
Expand All @@ -60,4 +66,4 @@ RUN /bin/bash -c "conda install -y -c conda-forge mamba && \

RUN echo "source activate quatradis" > ~/.bashrc
ENV PATH /opt/conda/envs/quatradis/bin:/home/quatradis/.local/bin:${PATH}
RUN pip install cython pysam pytest-cov semantic-version matplotlib scipy
RUN pip install cython pysam pytest-cov semantic-version matplotlib scipy
269 changes: 130 additions & 139 deletions README.md

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