diff --git a/workflows/Dockerfile b/workflows/Dockerfile deleted file mode 100644 index 62f7b54a404f846f2173a80315550d9bc220cf64..0000000000000000000000000000000000000000 --- a/workflows/Dockerfile +++ /dev/null @@ -1,150 +0,0 @@ -FROM nvidia/cuda:11.2.0-cudnn8-runtime-ubuntu20.04 -RUN useradd --create-home --shell /bin/bash helixer_user -RUN apt-get update -y -RUN apt-get install -y --no-install-recommends apt-utils -RUN apt-get install python3-dev -y -RUN apt-get install python3-pip -y -RUN apt-get install python3-venv -y -RUN apt-get install git -y -RUN apt-get install libhdf5-dev -y -RUN apt-get install curl -y -RUN apt-get install wget -y -RUN apt-get autoremove -y - -ARG DEBIAN_FRONTEND=noninteractive -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 gcc -O2 -fPIC -shared -Ilzf -I/usr/include/hdf5/serial/ lzf/*.c lzf_filter.c -lhdf5 -L/lib/x86_64-linux-gnu/hdf5/serial -o liblzf_filter.so -#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:${PATH}" -# -## --- Helixer and HelixerPost --- # -# -#WORKDIR /home/helixer_user/ -#RUN git clone -b v0.3.0a0 https://github.com/weberlab-hhu/Helixer.git Helixer -#RUN pip install --no-cache-dir -r /home/helixer_user/Helixer/requirements.txt -#RUN cd Helixer && pip install --no-cache-dir . -# -WORKDIR /home/helixer_user/ -#RUN git clone https://github.com/TonyBolger/HelixerPost.git -#RUN cd HelixerPost && git checkout d180ad8b353fa8da69342bdb924ecfaeea9464af -RUN mkdir bin -ENV PATH="/home/helixer_user/bin:${PATH}" -#RUN cd HelixerPost/helixer_post_bin && cargo build --release -#RUN mv /home/helixer_user/HelixerPost/target/release/helixer_post_bin /home/helixer_user/bin/ -#RUN rm -r /home/helixer_user/HelixerPost/target/release/ - - -# -RUN apt install r-base-core -y -#RUN apt install rstudio -y -RUN apt install vim gedit git libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev virtualenv python-dev cmake jellyfish python-tk libcurl4-openssl-dev libgit2-dev libssl-dev -y - -WORKDIR /home/helixer_user/ -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/helixer_user/bin/ - - -#SOFTWAREDIR=$PWD - -#mkdir bin -# the raw files -#find . -maxdepth 2 -type f -executable|xargs -I% cp % bin/ -# alphabetically through the downloads -#cp downloads/augustus.2.5.5/bin/* bin/ - -#find downloads/bowtie2-2.3.4.2-linux-x86_64/ -maxdepth 1 -type f\ -# -executable|xargs -I% cp % bin/ - -#find downloads/cd-hit-v4.6.8-2017-1208/ -maxdepth 2 -type f \ -# -executable|xargs -I% cp % bin/ - -#ln -s ../downloads/FastQC/fastqc bin/ - -#cp downloads/gffread/gffread bin/ - -#cd downloads/gmap-2018-07-04 -#./configure --prefix=$SOFTWAREDIR -#make -#make install -#cd ../.. - -#find downloads/hisat2-2.1.0 -maxdepth 1 -type f -executable |xargs -I% cp % bin/ - -#cp downloads/kallisto_linux-v0.44.0/kallisto bin/ - -#cp downloads/mash-Linux64-v2.0/mash bin/ - -#find downloads/minimap2-2.12_x64-linux/ -maxdepth 1 -type f -executable |xargs -I% cp % bin/ - -#find downloads/RNAseq_workshop_helpers/ -maxdepth 1 -type f -executable |xargs -I% cp % bin/ - -#ln -s ../downloads/salmon-0.11.2-linux_x86_64/bin/salmon bin/ - -#cd downloads/samtools-1.9 -#./configure --prefix=$SOFTWAREDIR && make && make install -#cd ../.. - -#ln -s ../downloads/trinityrnaseq-Trinity-v2.8.2/Trinity bin/ - -#echo "please add the following lines to your ~/.bashrc file" -#echo 'export PATH=$PATH:'$SOFTWAREDIR'/bin' -#echo 'export AUGUSTUS_CONFIG_PATH='$SOFTWAREDIR'/downloads/augustus.2.5.5/config/' - -WORKDIR /home/helixer_user/bin -RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit -RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat -RUN chmod +x blat -RUN chmod +x faToTwoBit - - -# --- classic bioinf --- # -WORKDIR /home/helixer_user/ -RUN apt install hisat2 -y -RUN apt install bowtie2 -y -RUN apt install augustus -y -RUN apt install gffread -y -RUN apt install fastqc -y -RUN apt install salmon -y -RUN apt install samtools -y -RUN apt install trinityrnaseq -y -RUN apt install minimap2 -y -RUN apt install mash -y -RUN apt install gmap -y -RUN apt install cd-hit -y - -# --- conda/python --- # - -FROM conda/miniconda3 -WORKDIR /home/helixer_user/ -RUN conda update conda -#RUN conda create -n anaCogent5.2 python=3.7 anaconda -#RUN conda init bash -#RUN conda activate anaCogent5.2 -RUN conda install python=3.8 -RUN conda install libgcc-ng=9.3 -RUN conda install anaconda -RUN conda update -n base -c defaults conda -y -RUN conda install biopython -y -#RUN conda install -c http://conda.anaconda.org/cgat bx-python -y -RUN pip install bx-python -#RUN conda install -c bioconda bx-python -y -RUN conda install -c bioconda isoseq3 -y -RUN conda install -c bioconda pbccs -y -RUN conda install -c bioconda pbcoretools -y -RUN conda install -c bioconda bamtools -y -RUN conda install -c bioconda pysam -y -RUN pip install HTSeq -USER helixer_user -CMD ["bash"] diff --git a/workflows/docker/Dockerfile b/workflows/docker/Dockerfile index fc7805f6bf9bcb102ba3a44188b99d28098b6741..8bbb527e62bcd3e5fad5958d184f4a6616d87951 100644 --- a/workflows/docker/Dockerfile +++ b/workflows/docker/Dockerfile @@ -1,6 +1,6 @@ #FROM nvidia/cuda:11.2.0-cudnn8-runtime-ubuntu20.04 FROM ubuntu:latest -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 install -y --no-install-recommends apt-utils RUN apt-get install python3-dev -y @@ -32,21 +32,21 @@ ENV PATH="/root/.cargo/bin:${PATH}" # --- Helixer and HelixerPost --- # -WORKDIR /home/ZIM-gast/ -RUN mkdir /home/ZIM-gast/repos -WORKDIR /home/ZIM-gast/repos +WORKDIR /home/zim-gast/ +RUN mkdir /home/zim-gast/repos +WORKDIR /home/zim-gast/repos RUN git clone -b v0.3.0a0 https://github.com/weberlab-hhu/Helixer.git Helixer -RUN pip install --no-cache-dir -r /home/ZIM-gast/repos/Helixer/requirements.txt +RUN pip install --no-cache-dir -r /home/zim-gast/repos/Helixer/requirements.txt RUN cd Helixer && pip install --no-cache-dir . -WORKDIR /home/ZIM-gast/repos +WORKDIR /home/zim-gast/repos RUN git clone https://github.com/TonyBolger/HelixerPost.git RUN cd HelixerPost && git checkout d180ad8b353fa8da69342bdb924ecfaeea9464af -RUN mkdir /home/ZIM-gast/bin -ENV PATH="/home/ZIM-gast/bin:${PATH}" +RUN mkdir /home/zim-gast/bin +ENV PATH="/home/zim-gast/bin:${PATH}" RUN cd HelixerPost/helixer_post_bin && cargo build --release -RUN mv /home/ZIM-gast/repos/HelixerPost/target/release/helixer_post_bin /home/ZIM-gast/bin/ -RUN rm -r /home/ZIM-gast/repos/HelixerPost/target/release/ +RUN mv /home/zim-gast/repos/HelixerPost/target/release/helixer_post_bin /home/zim-gast/bin/ +RUN rm -r /home/zim-gast/repos/HelixerPost/target/release/ # @@ -54,15 +54,15 @@ RUN apt install r-base-core -y #RUN apt install rstudio -y RUN apt install libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev cmake jellyfish python-tk libcurl4-openssl-dev libgit2-dev libssl-dev -y -WORKDIR /home/ZIM-gast/repos +WORKDIR /home/zim-gast/repos RUN git clone https://github.com/alisandra/RNAseq_workshop_helpers.git -RUN find RNAseq_workshop_helpers . -maxdepth 2 -type f -executable|xargs -I% cp % /home/ZIM-gast/bin/ +RUN find RNAseq_workshop_helpers . -maxdepth 2 -type f -executable|xargs -I% cp % /home/zim-gast/bin/ #echo "please add the following lines to your ~/.bashrc file" #echo 'export PATH=$PATH:'$SOFTWAREDIR'/bin' #echo 'export AUGUSTUS_CONFIG_PATH='$SOFTWAREDIR'/downloads/augustus.2.5.5/config/' -WORKDIR /home/ZIM-gast/bin +WORKDIR /home/zim-gast/bin RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat RUN chmod +x blat @@ -70,7 +70,7 @@ RUN chmod +x faToTwoBit # --- classic bioinf --- # -WORKDIR /home/ZIM-gast/ +WORKDIR /home/zim-gast/ RUN apt install hisat2 -y RUN apt install bowtie2 -y RUN apt install augustus -y @@ -98,19 +98,19 @@ RUN tar xvf bax2bam-0.0.11-0.tar.bz2 # kallisto RUN apt install libhdf5-dev m4 -y -WORKDIR /home/ZIM-gast/repos +WORKDIR /home/zim-gast/repos RUN curl -O -L http://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz RUN tar -xzf autoconf-2.69.tar.gz -WORKDIR /home/ZIM-gast/repos/autoconf-2.69 +WORKDIR /home/zim-gast/repos/autoconf-2.69 RUN ./configure RUN make RUN make install -WORKDIR /home/ZIM-gast/repos +WORKDIR /home/zim-gast/repos RUN git clone https://github.com/pachterlab/kallisto.git RUN mkdir kallisto/build -WORKDIR /home/ZIM-gast/repos/kallisto/build +WORKDIR /home/zim-gast/repos/kallisto/build ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/hdf5/serial/lib -RUN cmake -DCMAKE_INSTALL_PREFIX=/home/ZIM-gast/ -DUSE_HDF5=ON .. +RUN cmake -DCMAKE_INSTALL_PREFIX=/home/zim-gast/ -DUSE_HDF5=ON .. RUN make RUN make install # python @@ -120,29 +120,29 @@ RUN rm python_installs.sh # for virtualenv intro RUN pip install virtualenv -ENV PATH="/home/ZIM-gast/.local/bin:${PATH}" +ENV PATH="/home/zim-gast/.local/bin:${PATH}" # jars -RUN mkdir /home/ZIM-gast/sw -WORKDIR /home/ZIM-gast/sw +RUN mkdir /home/zim-gast/sw +WORKDIR /home/zim-gast/sw RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip RUN unzip Trimmomatic-0.39.zip RUN rm Trimmomatic-0.39.zip # cleanup -WORKDIR /home/ZIM-gast/ +WORKDIR /home/zim-gast/ RUN rm *.bz2 RUN rm -r info # shared folder -RUN mkdir /home/ZIM-gast/rnaseq-workshop +RUN mkdir /home/zim-gast/rnaseq-workshop RUN apt purge gmap -y RUN apt install gmap -y EXPOSE 8889 -USER ZIM-gast +USER zim-gast RUN echo "alias gmap='/usr/bin/gmap'" >> .bashrc CMD ["bash"]