#FROM nvidia/cuda:11.2.0-cudnn8-runtime-ubuntu20.04 FROM ubuntu:latest # Overide user name at build, if buil-arg no passed, will create user named `default` user ARG DOCKER_USER=zim-gast # Create a group and user RUN adduser $DOCKER_USER #RUN useradd --create-home --shell /bin/bash zim-gast RUN apt-get update -y RUN apt install python3-dev \ python3-pip \ git \ libhdf5-dev \ curl \ wget \ nano vim emacs -y RUN apt-get autoremove -y ARG DEBIAN_FRONTEND=noninteractive ENV TZ=Europe/Berlin RUN apt install libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev cmake jellyfish python-tk libcurl4-openssl-dev libgit2-dev libssl-dev -y RUN mkdir /home/$DOCKER_USER/repos && \ cd /home/$DOCKER_USER/repos && \ git clone https://github.com/alisandra/RNAseq_workshop_helpers.git && \ mkdir /home/$DOCKER_USER/bin && \ find RNAseq_workshop_helpers . -maxdepth 2 -type f -executable|xargs -I% cp % /home/$DOCKER_USER/bin/ #echo "please add the following lines to your ~/.bashrc file" #echo 'export PATH=$PATH:'$SOFTWAREDIR'/bin' #echo 'export AUGUSTUS_CONFIG_PATH='$SOFTWAREDIR'/downloads/augustus.2.5.5/config/' WORKDIR /home/$DOCKER_USER/bin RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit && chmod +x faToTwoBit && \ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat && chmod +x blat # --- classic bioinf --- # WORKDIR /home/$DOCKER_USER/ RUN apt install hisat2 \ bowtie2 \ augustus \ gffread \ fastqc \ salmon \ samtools \ minimap2 \ mash \ cd-hit tar bzip2 \ libhdf5-dev m4 -y # last ones are for kallisto # --- used to be conda, now binaries... --- # # for virtualenv intro ENV PATH="/home/$DOCKER_USER/.local/bin:${PATH}" RUN pip install HTSeq virtualenv RUN wget https://anaconda.org/bioconda/isoseq3/3.7.0/download/linux-64/isoseq3-3.7.0-h9ee0642_0.tar.bz2 && \ tar xvf isoseq3-3.7.0-h9ee0642_0.tar.bz2 && \ wget https://anaconda.org/bioconda/lima/2.6.0/download/linux-64/lima-2.6.0-h9ee0642_0.tar.bz2 && \ tar xvf lima-2.6.0-h9ee0642_0.tar.bz2 && \ wget https://anaconda.org/bioconda/pbccs/6.4.0/download/linux-64/pbccs-6.4.0-h9ee0642_0.tar.bz2 && \ tar xvf pbccs-6.4.0-h9ee0642_0.tar.bz2 && \ wget https://anaconda.org/bioconda/bax2bam/0.0.11/download/linux-64/bax2bam-0.0.11-0.tar.bz2 && \ tar xvf bax2bam-0.0.11-0.tar.bz2 # kallisto ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/hdf5/serial/lib RUN cd /home/$DOCKER_USER/repos && \ curl -O -L http://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz && \ tar -xzf autoconf-2.69.tar.gz && cd /home/$DOCKER_USER/repos/autoconf-2.69 && \ ./configure && make && make install && cd /home/$DOCKER_USER/repos && \ git clone https://github.com/pachterlab/kallisto.git && \ mkdir kallisto/build && \ cd /home/$DOCKER_USER/repos/kallisto/build && \ cmake -DCMAKE_INSTALL_PREFIX=/home/$DOCKER_USER/ -DUSE_HDF5=ON .. && make && make install # python COPY python_installs.sh ./ RUN ./python_installs.sh && rm python_installs.sh # jars RUN mkdir /home/$DOCKER_USER/sw && \ cd /home/$DOCKER_USER/sw && \ wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip && \ apt install unzip -y && \ unzip Trimmomatic-0.39.zip && \ rm Trimmomatic-0.39.zip # cleanup WORKDIR /home/$DOCKER_USER/ RUN rm *.bz2 && rm -r info # shared folder # rnaseq-workshop folder RUN wget https://github.com/git-lfs/git-lfs/releases/download/v3.2.0/git-lfs-linux-amd64-v3.2.0.tar.gz && \ mv git-lfs-linux-amd64-v3.2.0.tar.gz sw/ && \ cd /home/$DOCKER_USER/sw/ && \ tar xvf git-lfs-linux-amd64-v3.2.0.tar.gz && \ cd /home/$DOCKER_USER/sw/git-lfs-3.2.0/ && \ ./install.sh && \ rm ../git-lfs-linux-amd64-v3.2.0.tar.gz WORKDIR /home/$DOCKER_USER/ #RUN git clone https://git.nfdi4plants.org/brilator/rnaseq-workshop.git RUN mkdir /home/$DOCKER_USER/rnaseq-workshop RUN apt install gmap -y RUN rm -rf /var/lib/apt/lists/* EXPOSE 8889 COPY ./first.sh /home/$DOCKER_USER/ RUN chown $DOCKER_USER:$DOCKER_USER /home/$DOCKER_USER/first.sh RUN cd /home/$DOCKER_USER/repos/alisandra/cDNA_Cupcake && \ pip install . ENV PATH="/home/$DOCKER_USER/bin:${PATH}" USER $DOCKER_USER RUN git lfs install RUN echo "alias gmap='/usr/bin/gmap'" >> .bashrc CMD ["bash"]