From ff05dcecf3d65eb2d7a383021b46991dcd7366cd Mon Sep 17 00:00:00 2001
From: alisandra <alisandra.denton@hhu.de>
Date: Tue, 23 Aug 2022 16:05:57 +0200
Subject: [PATCH] by urgent need shrinkage, dropped Helixer
---
workflows/maindocker/Dockerfile | 87 +++++++++------------------------
1 file changed, 23 insertions(+), 64 deletions(-)
diff --git a/workflows/maindocker/Dockerfile b/workflows/maindocker/Dockerfile
index 942710a..d48e6cd 100644
--- a/workflows/maindocker/Dockerfile
+++ b/workflows/maindocker/Dockerfile
@@ -10,65 +10,31 @@ RUN adduser $DOCKER_USER
#RUN useradd --create-home --shell /bin/bash zim-gast
RUN apt-get update -y
-RUN apt-get install -y --no-install-recommends apt-utils
-RUN apt-get install python3-dev -y
-RUN apt-get install python3-pip -y
-RUN apt-get install python3-venv -y
-RUN apt-get install git -y
-RUN apt-get install libhdf5-dev -y
-RUN apt-get install curl -y
-RUN apt-get install wget -y
-RUN apt install nano vim emacs -y
+RUN apt install python3-dev \
+ python3-pip \
+ git \
+ libhdf5-dev \
+ curl \
+ wget \
+ nano vim emacs -y
RUN apt-get autoremove -y
ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=Europe/Berlin
-# --- prep for hdf5 for HelixerPost --- #
-WORKDIR /tmp/
-RUN curl -L https://github.com/h5py/h5py/releases/download/3.2.1/h5py-3.2.1.tar.gz --output h5py-3.2.1.tar.gz
-RUN tar -xzvf h5py-3.2.1.tar.gz
-RUN cd h5py-3.2.1/lzf/ && gcc -O2 -fPIC -shared -Ilzf -I/usr/include/hdf5/serial/ lzf/*.c lzf_filter.c -lhdf5_cpp -L/lib/x86_64-linux-gnu/hdf5/serial -o liblzf_filter.so
-RUN mkdir /usr/lib/x86_64-linux-gnu/hdf5/plugins && mv h5py-3.2.1/lzf/liblzf_filter.so /usr/lib/x86_64-linux-gnu/hdf5/plugins
-RUN rm -r /tmp/h5py*
-
-# --- rust install for HelixerPost --- #
-RUN curl https://sh.rustup.rs -sSf > rustup.sh
-RUN chmod 755 rustup.sh
-RUN ./rustup.sh -y
-RUN rm rustup.sh
-ENV PATH="/root/.cargo/bin:${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/$DOCKER_USER/repos/HelixerPost/target/release/
RUN apt install libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev cmake jellyfish python-tk libcurl4-openssl-dev libgit2-dev libssl-dev -y
WORKDIR /home/$DOCKER_USER/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/$DOCKER_USER/bin/
+RUN mkdir /home/$DOCKER_USER/bin && find RNAseq_workshop_helpers . -maxdepth 2 -type f -executable|xargs -I% cp % /home/$DOCKER_USER/bin/
#echo "please add the following lines to your ~/.bashrc file"
#echo 'export PATH=$PATH:'$SOFTWAREDIR'/bin'
#echo 'export AUGUSTUS_CONFIG_PATH='$SOFTWAREDIR'/downloads/augustus.2.5.5/config/'
WORKDIR /home/$DOCKER_USER/bin
-RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit && chmod +x faToTwoBit
-RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat && chmod +x blat
+RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit && chmod +x faToTwoBit && \
+ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat && chmod +x blat
# --- classic bioinf --- #
@@ -103,21 +69,15 @@ WORKDIR /home/$DOCKER_USER/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/$DOCKER_USER/repos/autoconf-2.69
-RUN ./configure
-RUN make
-RUN make install
+RUN ./configure && make && make install
WORKDIR /home/$DOCKER_USER/repos
-RUN git clone https://github.com/pachterlab/kallisto.git
-RUN mkdir kallisto/build
+RUN git clone https://github.com/pachterlab/kallisto.git && mkdir 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
-RUN cmake -DCMAKE_INSTALL_PREFIX=/home/$DOCKER_USER/ -DUSE_HDF5=ON ..
-RUN make
-RUN make install
+RUN cmake -DCMAKE_INSTALL_PREFIX=/home/$DOCKER_USER/ -DUSE_HDF5=ON .. && make && make install
# python
COPY python_installs.sh ./
-RUN ./python_installs.sh
-RUN rm python_installs.sh
+RUN ./python_installs.sh && rm python_installs.sh
# for virtualenv intro
RUN pip install virtualenv
@@ -126,26 +86,25 @@ ENV PATH="/home/$DOCKER_USER/.local/bin:${PATH}"
# jars
RUN mkdir /home/$DOCKER_USER/sw
WORKDIR /home/$DOCKER_USER/sw
-RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
-RUN apt install unzip -y
-RUN unzip Trimmomatic-0.39.zip
-RUN rm Trimmomatic-0.39.zip
+RUN 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/$DOCKER_USER/
-RUN rm *.bz2
-RUN rm -r info
+RUN rm *.bz2 && rm -r info
# shared folder
# rnaseq-workshop folder
-RUN wget https://github.com/git-lfs/git-lfs/releases/download/v3.2.0/git-lfs-linux-amd64-v3.2.0.tar.gz
-RUN mv git-lfs-linux-amd64-v3.2.0.tar.gz sw/
+RUN wget https://github.com/git-lfs/git-lfs/releases/download/v3.2.0/git-lfs-linux-amd64-v3.2.0.tar.gz && \
+ mv git-lfs-linux-amd64-v3.2.0.tar.gz sw/
WORKDIR /home/$DOCKER_USER/sw/
RUN tar xvf git-lfs-linux-amd64-v3.2.0.tar.gz
WORKDIR /home/$DOCKER_USER/sw/git-lfs-3.2.0/
-RUN ./install.sh
-RUN rm ../git-lfs-linux-amd64-v3.2.0.tar.gz
+RUN ./install.sh && \
+ rm ../git-lfs-linux-amd64-v3.2.0.tar.gz
WORKDIR /home/$DOCKER_USER/
#RUN git clone https://git.nfdi4plants.org/brilator/rnaseq-workshop.git
--
GitLab