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Commit ff05dcec authored by Alisandra Denton's avatar Alisandra Denton
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by urgent need shrinkage, dropped Helixer

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...@@ -10,65 +10,31 @@ RUN adduser $DOCKER_USER ...@@ -10,65 +10,31 @@ RUN adduser $DOCKER_USER
#RUN useradd --create-home --shell /bin/bash zim-gast #RUN useradd --create-home --shell /bin/bash zim-gast
RUN apt-get update -y RUN apt-get update -y
RUN apt-get install -y --no-install-recommends apt-utils RUN apt install python3-dev \
RUN apt-get install python3-dev -y python3-pip \
RUN apt-get install python3-pip -y git \
RUN apt-get install python3-venv -y libhdf5-dev \
RUN apt-get install git -y curl \
RUN apt-get install libhdf5-dev -y wget \
RUN apt-get install curl -y nano vim emacs -y
RUN apt-get install wget -y
RUN apt install nano vim emacs -y
RUN apt-get autoremove -y RUN apt-get autoremove -y
ARG DEBIAN_FRONTEND=noninteractive ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=Europe/Berlin ENV TZ=Europe/Berlin
# --- prep for hdf5 for HelixerPost --- #
WORKDIR /tmp/
RUN curl -L https://github.com/h5py/h5py/releases/download/3.2.1/h5py-3.2.1.tar.gz --output h5py-3.2.1.tar.gz
RUN tar -xzvf h5py-3.2.1.tar.gz
RUN cd h5py-3.2.1/lzf/ && gcc -O2 -fPIC -shared -Ilzf -I/usr/include/hdf5/serial/ lzf/*.c lzf_filter.c -lhdf5_cpp -L/lib/x86_64-linux-gnu/hdf5/serial -o liblzf_filter.so
RUN mkdir /usr/lib/x86_64-linux-gnu/hdf5/plugins && mv h5py-3.2.1/lzf/liblzf_filter.so /usr/lib/x86_64-linux-gnu/hdf5/plugins
RUN rm -r /tmp/h5py*
# --- rust install for HelixerPost --- #
RUN curl https://sh.rustup.rs -sSf > rustup.sh
RUN chmod 755 rustup.sh
RUN ./rustup.sh -y
RUN rm rustup.sh
ENV PATH="/root/.cargo/bin:${PATH}"
# --- Helixer and HelixerPost --- #
WORKDIR /home/$DOCKER_USER/
RUN mkdir /home/$DOCKER_USER/repos
WORKDIR /home/$DOCKER_USER/repos
RUN git clone -b v0.3.0a0 https://github.com/weberlab-hhu/Helixer.git Helixer
RUN pip install --no-cache-dir -r /home/$DOCKER_USER/repos/Helixer/requirements.txt
RUN cd Helixer && pip install --no-cache-dir .
WORKDIR /home/$DOCKER_USER/repos
RUN git clone https://github.com/TonyBolger/HelixerPost.git
RUN cd HelixerPost && git checkout d180ad8b353fa8da69342bdb924ecfaeea9464af
RUN mkdir /home/$DOCKER_USER/bin
ENV PATH="/home/$DOCKER_USER/bin:${PATH}"
RUN cd HelixerPost/helixer_post_bin && cargo build --release
RUN mv /home/$DOCKER_USER/repos/HelixerPost/target/release/helixer_post_bin /home/$DOCKER_USER/bin/
RUN rm -r /home/$DOCKER_USER/repos/HelixerPost/target/release/
RUN apt install libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev cmake jellyfish python-tk libcurl4-openssl-dev libgit2-dev libssl-dev -y RUN apt install libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev cmake jellyfish python-tk libcurl4-openssl-dev libgit2-dev libssl-dev -y
WORKDIR /home/$DOCKER_USER/repos WORKDIR /home/$DOCKER_USER/repos
RUN git clone https://github.com/alisandra/RNAseq_workshop_helpers.git RUN git clone https://github.com/alisandra/RNAseq_workshop_helpers.git
RUN find RNAseq_workshop_helpers . -maxdepth 2 -type f -executable|xargs -I% cp % /home/$DOCKER_USER/bin/ RUN 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 "please add the following lines to your ~/.bashrc file"
#echo 'export PATH=$PATH:'$SOFTWAREDIR'/bin' #echo 'export PATH=$PATH:'$SOFTWAREDIR'/bin'
#echo 'export AUGUSTUS_CONFIG_PATH='$SOFTWAREDIR'/downloads/augustus.2.5.5/config/' #echo 'export AUGUSTUS_CONFIG_PATH='$SOFTWAREDIR'/downloads/augustus.2.5.5/config/'
WORKDIR /home/$DOCKER_USER/bin WORKDIR /home/$DOCKER_USER/bin
RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit && chmod +x faToTwoBit RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit && chmod +x faToTwoBit && \
RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat && chmod +x blat wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat && chmod +x blat
# --- classic bioinf --- # # --- classic bioinf --- #
...@@ -103,21 +69,15 @@ WORKDIR /home/$DOCKER_USER/repos ...@@ -103,21 +69,15 @@ WORKDIR /home/$DOCKER_USER/repos
RUN curl -O -L http://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz RUN curl -O -L http://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz
RUN tar -xzf autoconf-2.69.tar.gz RUN tar -xzf autoconf-2.69.tar.gz
WORKDIR /home/$DOCKER_USER/repos/autoconf-2.69 WORKDIR /home/$DOCKER_USER/repos/autoconf-2.69
RUN ./configure RUN ./configure && make && make install
RUN make
RUN make install
WORKDIR /home/$DOCKER_USER/repos WORKDIR /home/$DOCKER_USER/repos
RUN git clone https://github.com/pachterlab/kallisto.git RUN git clone https://github.com/pachterlab/kallisto.git && mkdir kallisto/build
RUN mkdir kallisto/build
WORKDIR /home/$DOCKER_USER/repos/kallisto/build WORKDIR /home/$DOCKER_USER/repos/kallisto/build
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/hdf5/serial/lib ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/hdf5/serial/lib
RUN cmake -DCMAKE_INSTALL_PREFIX=/home/$DOCKER_USER/ -DUSE_HDF5=ON .. RUN cmake -DCMAKE_INSTALL_PREFIX=/home/$DOCKER_USER/ -DUSE_HDF5=ON .. && make && make install
RUN make
RUN make install
# python # python
COPY python_installs.sh ./ COPY python_installs.sh ./
RUN ./python_installs.sh RUN ./python_installs.sh && rm python_installs.sh
RUN rm python_installs.sh
# for virtualenv intro # for virtualenv intro
RUN pip install virtualenv RUN pip install virtualenv
...@@ -126,26 +86,25 @@ ENV PATH="/home/$DOCKER_USER/.local/bin:${PATH}" ...@@ -126,26 +86,25 @@ ENV PATH="/home/$DOCKER_USER/.local/bin:${PATH}"
# jars # jars
RUN mkdir /home/$DOCKER_USER/sw RUN mkdir /home/$DOCKER_USER/sw
WORKDIR /home/$DOCKER_USER/sw WORKDIR /home/$DOCKER_USER/sw
RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip && \
RUN apt install unzip -y apt install unzip -y && \
RUN unzip Trimmomatic-0.39.zip unzip Trimmomatic-0.39.zip && \
RUN rm Trimmomatic-0.39.zip rm Trimmomatic-0.39.zip
# cleanup # cleanup
WORKDIR /home/$DOCKER_USER/ WORKDIR /home/$DOCKER_USER/
RUN rm *.bz2 RUN rm *.bz2 && rm -r info
RUN rm -r info
# shared folder # shared folder
# rnaseq-workshop 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 RUN wget https://github.com/git-lfs/git-lfs/releases/download/v3.2.0/git-lfs-linux-amd64-v3.2.0.tar.gz && \
RUN mv git-lfs-linux-amd64-v3.2.0.tar.gz sw/ mv git-lfs-linux-amd64-v3.2.0.tar.gz sw/
WORKDIR /home/$DOCKER_USER/sw/ WORKDIR /home/$DOCKER_USER/sw/
RUN tar xvf git-lfs-linux-amd64-v3.2.0.tar.gz RUN tar xvf git-lfs-linux-amd64-v3.2.0.tar.gz
WORKDIR /home/$DOCKER_USER/sw/git-lfs-3.2.0/ WORKDIR /home/$DOCKER_USER/sw/git-lfs-3.2.0/
RUN ./install.sh RUN ./install.sh && \
RUN rm ../git-lfs-linux-amd64-v3.2.0.tar.gz rm ../git-lfs-linux-amd64-v3.2.0.tar.gz
WORKDIR /home/$DOCKER_USER/ WORKDIR /home/$DOCKER_USER/
#RUN git clone https://git.nfdi4plants.org/brilator/rnaseq-workshop.git #RUN git clone https://git.nfdi4plants.org/brilator/rnaseq-workshop.git
......
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