diff --git a/rnaseq/ccbr_build_rnaseq/Dockerfile b/rnaseq/ccbr_build_rnaseq/Dockerfile deleted file mode 100644 index a5d88ab..0000000 --- a/rnaseq/ccbr_build_rnaseq/Dockerfile +++ /dev/null @@ -1,54 +0,0 @@ -# ccbr_build_rnaseq Dockerfile (v0.0.1) -FROM ubuntu:18.04 - -MAINTAINER , - -RUN mkdir -p /data2 -RUN mkdir -p /opt2/ucsc/ - -# Update apt-get before downloading packages -RUN apt-get update && \ - apt-get upgrade -y - -# Install dependencies: python (2.7), python (3.6) and pip3, wget to download UCSC binaries -# samtools to install libkrb5.so.3: open shared object file (needed bby UCSC tools) -RUN DEBIAN_FRONTEND=noninteractive apt-get install --yes \ - wget \ - python \ - bedtools \ - samtools \ - python3 \ - python3-pip \ - locales && \ -apt-get clean && \ - rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* - -WORKDIR /opt2/ucsc - -# Get a controlled release of UCSC tool from my mirror: https://github.com/skchronicles/ucsc_mirror/ -RUN wget https://github.com/skchronicles/ucsc_mirror/raw/main/bedSort && \ - wget https://github.com/skchronicles/ucsc_mirror/raw/main/genePredToBed && \ - wget https://github.com/skchronicles/ucsc_mirror/raw/main/gtfToGenePred && \ - chmod a+rx /opt2/ucsc/* - -# Pip install required Python dependencies -## argparse -## Bio -## HTSeq -## numpy -## scipy -## pysam -RUN pip3 install --upgrade pip -RUN pip3 install bio==0.4.1 biopython==1.78 certifi==2020.12.5 chardet==4.0.0 HTSeq==0.13.5 idna==2.10 numpy==1.19.5 pysam==0.16.0.1 requests==2.25.1 scipy==1.5.4 urllib3==1.26.4 - -# Set environment variable(s) -# Configure "locale", see https://github.com/rocker-org/rocker/issues/19 -RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \ - && locale-gen en_US.utf8 \ - && /usr/sbin/update-locale LANG=en_US.UTF-8 - -# Add UCSC tools to PATH -ENV PATH="/opt2/ucsc":$PATH - -COPY Dockerfile /opt2/ -WORKDIR /data2 diff --git a/rnaseq/ccbr_build_rnaseq/Dockerfile b/rnaseq/ccbr_build_rnaseq/Dockerfile new file mode 120000 index 0000000..45535df --- /dev/null +++ b/rnaseq/ccbr_build_rnaseq/Dockerfile @@ -0,0 +1 @@ +Dockerfile.v2 \ No newline at end of file diff --git a/rnaseq/ccbr_build_rnaseq/Dockerfile.v1 b/rnaseq/ccbr_build_rnaseq/Dockerfile.v1 new file mode 100644 index 0000000..5e4719e --- /dev/null +++ b/rnaseq/ccbr_build_rnaseq/Dockerfile.v1 @@ -0,0 +1,54 @@ +# ccbr_build_rnaseq Dockerfile (v0.0.1) +FROM ubuntu:18.04 + +MAINTAINER , + +RUN mkdir -p /data2 +RUN mkdir -p /opt2/ucsc/ + +# Update apt-get before downloading packages +RUN apt-get update && \ + apt-get upgrade -y + +# Install dependencies: python (2.7), python (3.6) and pip3, wget to download UCSC binaries +# samtools to install libkrb5.so.3: open shared object file (needed bby UCSC tools) +RUN DEBIAN_FRONTEND=noninteractive apt-get install --yes \ + wget \ + python \ + bedtools \ + samtools \ + python3 \ + python3-pip \ + locales && \ +apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +WORKDIR /opt2/ucsc + +# Get a controlled release of UCSC tool from my mirror: https://github.com/skchronicles/ucsc_mirror/ +RUN wget https://github.com/skchronicles/ucsc_mirror/raw/main/bedSort && \ + wget https://github.com/skchronicles/ucsc_mirror/raw/main/genePredToBed && \ + wget https://github.com/skchronicles/ucsc_mirror/raw/main/gtfToGenePred && \ + chmod a+rx /opt2/ucsc/* + +# Pip install required Python dependencies +## argparse +## Bio +## HTSeq +## numpy +## scipy +## pysam +RUN pip3 install --upgrade pip +RUN pip3 install bio==0.4.1 biopython==1.78 certifi==2020.12.5 chardet==4.0.0 HTSeq==0.13.5 idna==2.10 numpy==1.19.5 pysam==0.16.0.1 requests==2.25.1 scipy==1.5.4 urllib3==1.26.4 + +# Set environment variable(s) +# Configure "locale", see https://github.com/rocker-org/rocker/issues/19 +RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \ + && locale-gen en_US.utf8 \ + && /usr/sbin/update-locale LANG=en_US.UTF-8 + +# Add UCSC tools to PATH +ENV PATH="/opt2/ucsc":$PATH + +COPY Dockerfile /opt2/ +WORKDIR /data2 diff --git a/rnaseq/ccbr_build_rnaseq/Dockerfile.v2 b/rnaseq/ccbr_build_rnaseq/Dockerfile.v2 new file mode 100644 index 0000000..2d1129b --- /dev/null +++ b/rnaseq/ccbr_build_rnaseq/Dockerfile.v2 @@ -0,0 +1,38 @@ +# ccbr_build_rnaseq Dockerfile (v2) +FROM nciccbr/ccbr_ubuntu_22.04:v4 + +# build time variables +ARG BUILD_DATE="000000" +ENV BUILD_DATE=${BUILD_DATE} +ARG BUILD_TAG="000000" +ENV BUILD_TAG=${BUILD_TAG} +ARG REPONAME="000000" +ENV REPONAME=${REPONAME} + +# Install conda and give write permissions to conda folder +RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \ + wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \ + /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \ + rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/ +ENV PATH="/opt2/conda/bin:$PATH" +RUN conda config --add channels bioconda +RUN conda config --add channels conda-forge +RUN conda config --add channels r +RUN conda upgrade conda + +RUN mamba install -c bioconda \ + ucsc-bedsort \ + 'bio>=0.4.1' \ + 'biopython>=1.78' \ + 'certifi>=2020.12.5' \ + 'chardet>=4.0.0' \ + 'HTSeq>=0.13.5' \ + 'idna>=2.10' \ + 'numpy>=1.19.5' \ + 'pysam>=0.16.0.1' \ + 'requests>=2.25.1' \ + 'scipy>=1.5.4' \ + 'urllib3==1.26.4' + +COPY Dockerfile /opt2/ +WORKDIR /data2 diff --git a/rnaseq/ccbr_build_rnaseq/meta.yml b/rnaseq/ccbr_build_rnaseq/meta.yml new file mode 100644 index 0000000..73e44dd --- /dev/null +++ b/rnaseq/ccbr_build_rnaseq/meta.yml @@ -0,0 +1,4 @@ +dockerhub_namespace: nciccbr +image_name: ccbr_build_rnaseq +version: v2 +container: "$(dockerhub_namespace)/$(image_name):$(version)"