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jen-reevejen-reeve
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removing all non-apt installs
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‎docker/Dockerfile‎

Lines changed: 70 additions & 70 deletions
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@@ -71,76 +71,76 @@ RUN git clone https://github.com/nesi/training-environment-k8s-utils.git /opt/oo
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RUN echo "#!/bin/bash" > /bin/module \
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&& chmod +x /bin/module
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# Install Python-based tools in a virtual environment
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RUN python3 -m venv /opt/venv && \
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/opt/venv/bin/pip install --upgrade pip && \
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/opt/venv/bin/pip install \
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multiqc \
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cutadapt && \
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# Create symlinks to the venv binaries
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ln -s /opt/venv/bin/multiqc /usr/local/bin/ && \
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ln -s /opt/venv/bin/cutadapt /usr/local/bin/
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# Install FastQC
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RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip && \
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unzip fastqc_v0.12.1.zip && \
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mv FastQC /opt/ && \
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chmod +x /opt/FastQC/fastqc && \
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ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
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rm fastqc_v0.12.1.zip
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# Install samtools
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RUN wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 && \
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tar -xjf samtools-1.18.tar.bz2 && \
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cd samtools-1.18 && \
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./configure --prefix=/usr/local && \
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make && \
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make install && \
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cd .. && \
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rm -rf samtools-1.18*
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# Install hisat2
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RUN wget https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download -O hisat2-2.2.1-Linux_x86_64.zip && \
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unzip hisat2-2.2.1-Linux_x86_64.zip && \
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cd hisat2-2.2.1/ && \
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make && \
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cd .. && \
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mv hisat2-2.2.1/hisat2* /usr/local/bin/ && \
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mv hisat2-2.2.1/extract_exons* /usr/local/bin/ && \
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rm -rf hisat2-2.2.1*
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# Install subread
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RUN wget https://sourceforge.net/projects/subread/files/subread-2.0.3/subread-2.0.3-Linux-x86_64.tar.gz/download -O subread-2.0.3-Linux-x86_64.tar.gz && \
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tar -xzf subread-2.0.3-Linux-x86_64.tar.gz && \
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cp -r subread-2.0.3-Linux-x86_64/bin/* /usr/local/bin/ && \
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rm -rf subread-2.0.3*
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# Install bamtools
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RUN apt-get update && apt-get install -y cmake && \
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git clone https://github.com/pezmaster31/bamtools.git && \
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cd bamtools && \
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mkdir build && \
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cd build && \
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cmake -DCMAKE_INSTALL_PREFIX=/usr/local .. && \
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make && \
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make install && \
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cd ../.. && \
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rm -rf bamtools && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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# Install salmon
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RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v1.10.0/salmon-1.10.0_linux_x86_64.tar.gz && \
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tar -xzf salmon-1.10.0_linux_x86_64.tar.gz && \
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cp -r salmon-latest_linux_x86_64/bin/* /usr/local/bin/ && \
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cp -r salmon-latest_linux_x86_64/lib/* /usr/local/lib/ && \
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rm -rf salmon-1.10.1*
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# Install STAR with required dependencies
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RUN wget https://github.com/alexdobin/STAR/releases/download/2.7.11b/STAR_2.7.11b.zip && \
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unzip STAR_2.7.11b.zip && \
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cp STAR_2.7.11b/Linux_x86_64/STAR* /usr/local/bin/ && \
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rm -rf STAR_2.7.11b*
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# # Install Python-based tools in a virtual environment
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# RUN python3 -m venv /opt/venv && \
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# /opt/venv/bin/pip install --upgrade pip && \
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# /opt/venv/bin/pip install \
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# multiqc \
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# cutadapt && \
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# # Create symlinks to the venv binaries
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# ln -s /opt/venv/bin/multiqc /usr/local/bin/ && \
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# ln -s /opt/venv/bin/cutadapt /usr/local/bin/
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# # Install FastQC
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# RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip && \
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# unzip fastqc_v0.12.1.zip && \
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# mv FastQC /opt/ && \
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# chmod +x /opt/FastQC/fastqc && \
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# ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
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# rm fastqc_v0.12.1.zip
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# # Install samtools
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# RUN wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 && \
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# tar -xjf samtools-1.18.tar.bz2 && \
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# cd samtools-1.18 && \
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# ./configure --prefix=/usr/local && \
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# make && \
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# make install && \
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# cd .. && \
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# rm -rf samtools-1.18*
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# # Install hisat2
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# RUN wget https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download -O hisat2-2.2.1-Linux_x86_64.zip && \
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# unzip hisat2-2.2.1-Linux_x86_64.zip && \
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# cd hisat2-2.2.1/ && \
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# make && \
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# cd .. && \
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# mv hisat2-2.2.1/hisat2* /usr/local/bin/ && \
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# mv hisat2-2.2.1/extract_exons* /usr/local/bin/ && \
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# rm -rf hisat2-2.2.1*
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# # Install subread
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# RUN wget https://sourceforge.net/projects/subread/files/subread-2.0.3/subread-2.0.3-Linux-x86_64.tar.gz/download -O subread-2.0.3-Linux-x86_64.tar.gz && \
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# tar -xzf subread-2.0.3-Linux-x86_64.tar.gz && \
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# cp -r subread-2.0.3-Linux-x86_64/bin/* /usr/local/bin/ && \
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# rm -rf subread-2.0.3*
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# # Install bamtools
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# RUN apt-get update && apt-get install -y cmake && \
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# git clone https://github.com/pezmaster31/bamtools.git && \
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# cd bamtools && \
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# mkdir build && \
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# cd build && \
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# cmake -DCMAKE_INSTALL_PREFIX=/usr/local .. && \
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# make && \
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# make install && \
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# cd ../.. && \
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# rm -rf bamtools && \
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# apt-get clean && rm -rf /var/lib/apt/lists/*
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# # Install salmon
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# RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v1.10.0/salmon-1.10.0_linux_x86_64.tar.gz && \
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# tar -xzf salmon-1.10.0_linux_x86_64.tar.gz && \
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# cp -r salmon-latest_linux_x86_64/bin/* /usr/local/bin/ && \
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# cp -r salmon-latest_linux_x86_64/lib/* /usr/local/lib/ && \
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# rm -rf salmon-1.10.1*
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# # Install STAR with required dependencies
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# RUN wget https://github.com/alexdobin/STAR/releases/download/2.7.11b/STAR_2.7.11b.zip && \
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# unzip STAR_2.7.11b.zip && \
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# cp STAR_2.7.11b/Linux_x86_64/STAR* /usr/local/bin/ && \
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# rm -rf STAR_2.7.11b*
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# # Install QualiMap (resilient)
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# RUN set -eux; \

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