Merge pull request #41 from CCBR/build-rnaseq-fix-gtf

fix: upgrade build_rnaseq docker for newer Python version

rnaseq/ccbr_build_rnaseq/Dockerfile

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+Dockerfile.v2

rnaseq/ccbr_build_rnaseq/Dockerfile.v1

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+# ccbr_build_rnaseq Dockerfile (v0.0.1)
+FROM ubuntu:18.04
+
+MAINTAINER <vishal.koparde@nih.gov>, <kuhnsa@nih.gov>
+
+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

rnaseq/ccbr_build_rnaseq/Dockerfile.v2

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+# 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

rnaseq/ccbr_build_rnaseq/meta.yml

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+dockerhub_namespace: nciccbr
+image_name: ccbr_build_rnaseq
+version: v2
+container: "$(dockerhub_namespace)/$(image_name):$(version)"