Commit b9de66b0 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

cleanup and added gtdbtk

parent 830a04a9
...@@ -16,56 +16,11 @@ LABEL tags="Base" ...@@ -16,56 +16,11 @@ LABEL tags="Base"
ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_US.UTF-8 ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_US.UTF-8
# Install the CWL runner (cwltool) # Some default needed stuff
RUN apt-get update && apt-get install -y wget curl pigz nodejs build-essential cpanminus git python3 python3-dev python3-distutils && \ RUN apt-get update && apt-get install -y git build-essential curl wget nano htop pigz zip unzip
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py && \
pip3 install cwltool &&\
cwltool --version && pip install html5lib
# Enable icommands
RUN pip install python-irodsclient --upgrade && \
apt-get update && apt-get install -y gnupg && \
wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
echo "# /etc/apt/sources.list.d/renci-irods.list" | tee -a /etc/apt/sources.list.d/renci-irods.list && \
echo "deb [arch=amd64] https://packages.irods.org/apt/ xenial main" | tee -a /etc/apt/sources.list.d/renci-irods.list && \
apt-get update && apt-get install -y irods-icommands
# Install Java via sdkman # Install the CWL runner (cwltool) and python and pip
RUN apt-get update RUN apt-get update && apt-get install -y nodejs cpanminus python3 python3-dev python3-distutils && \
RUN apt-get -qq -y install \
curl \
unzip \
zip
RUN rm /bin/sh && ln -s /bin/bash /bin/sh
RUN apt-get -qq -y install curl
RUN curl -s https://get.sdkman.io | bash
RUN chmod a+x "$HOME/.sdkman/bin/sdkman-init.sh"
RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\
sdk install java 11.0.9.fx-zulu &&\
sdk install gradle 6.7 &&\
sdk install maven 3.6.3
# Other packages
# Base Image
FROM ubuntu:18.04
# Metadata
LABEL base.image="docker-registry.wur.nl/unlock/docker"
LABEL version="1"
LABEL software="BASE 1.0"
LABEL software.version="0.0.0"
LABEL description="IRODS base image for UNLOCK"
LABEL website="https://m-unlock.gitlab.io"
LABEL documentation="NA"
LABEL license="NA"
LABEL tags="Base"
# ARG cwltool_version=3.0.20200720165847
ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_US.UTF-8
# Install the CWL runner (cwltool) and pip
RUN apt-get update && apt-get install -y wget curl pigz nodejs build-essential cpanminus git python3 python3-dev python3-distutils && \
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py && \ curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py && \
pip3 install cwltool &&\ pip3 install cwltool &&\
cwltool --version && pip install html5lib cwltool --version && pip install html5lib
...@@ -79,13 +34,13 @@ RUN pip install python-irodsclient --upgrade && \ ...@@ -79,13 +34,13 @@ RUN pip install python-irodsclient --upgrade && \
apt-get update && apt-get install -y irods-icommands apt-get update && apt-get install -y irods-icommands
# Install Java via sdkman # Install Java via sdkman
RUN apt-get update # RUN apt-get update
RUN apt-get -qq -y install \ # RUN apt-get -qq -y install \
curl \ # curl \
unzip \ # unzip \
zip # zip
RUN rm /bin/sh && ln -s /bin/bash /bin/sh RUN rm /bin/sh && ln -s /bin/bash /bin/sh
RUN apt-get -qq -y install curl #RUN apt-get -qq -y install curl
RUN curl -s https://get.sdkman.io | bash RUN curl -s https://get.sdkman.io | bash
RUN chmod a+x "$HOME/.sdkman/bin/sdkman-init.sh" RUN chmod a+x "$HOME/.sdkman/bin/sdkman-init.sh"
RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\ RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\
...@@ -95,25 +50,39 @@ RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\ ...@@ -95,25 +50,39 @@ RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\
# Other packages # Other packages
# R # R
RUN apt install -y software-properties-common && \ RUN apt-get update && apt-get install -y software-properties-common && \
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \ apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/' && \ add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/' && \
apt update && \ apt update && \
apt install -y r-base apt install -y r-base
# FastqPuri (RNAseq pre-processing) dependencies ######################################
# RUN R -e "install.packages(c('pheatmap', 'knitr', 'rmarkdown' ,'stringr'))" ####### ANALYSIS TOOLS SECTION #######
# Quast ## Quast
RUN pip install quast RUN pip install quast
# Fix locale issue with quast # Fix locale issue with quast
RUN apt-get clean && apt-get update && apt-get install -y locales nano htop libfontconfig1 && locale-gen en_US.UTF-8 && dpkg-reconfigure locales RUN apt-get clean && apt-get update && apt-get install -y locales libfontconfig1 && locale-gen en_US.UTF-8 && dpkg-reconfigure locales
# CheckM ## CheckM
ENV PATH=$PATH:/unlock/infrastructure/binaries/hmmer/hmmer-3.3.2/bin/:/unlock/infrastructure/binaries/pplacer/pplacer-Linux-v1.1.alpha17/bin/:/unlock/infrastructure/binaries/prodigal/v2.6.3/
RUN pip3 install pysam numpy matplotlib checkm-genome && \ RUN pip3 install pysam numpy matplotlib checkm-genome && \
checkm data setRoot /unlock/references/databases/CheckM/ checkm data setRoot /unlock/references/databases/CheckM/
## GTDB-Tk
RUN python3 -m pip install gtdbtk
ENV GTDBTK_DATA_PATH=/unlock/references/databases/GTDBTK/release202/
## Needed for faTools
RUN sudo ln -s /usr/lib/x86_64-linux-gnu/libpng16.so.16.34.0 /usr/lib/x86_64-linux-gnu/libpng12.so.0
## SET PATH ##
ENV CHECKM=/unlock/infrastructure/binaries/hmmer/hmmer-3.3.2/bin:/unlock/infrastructure/binaries/pplacer/pplacer-Linux-v1.1.alpha17/bin:/unlock/infrastructure/binaries/prodigal/v2.6.3
# note: CheckM and GTDB-Tk overlap with hmmer,prodigal and are not added to GTDBTK
ENV GTDBTK=/unlock/infrastructure/binaries/Mash/mash-Linux64-v2.3:/unlock/infrastructure/binaries/FastTree/FastTree_v2.1.11:/unlock/infrastructure/binaries/Mash/mash-Linux64-v2.3:/unlock/infrastructure/binaries/fastANI/fastANI_v1.33
ENV PATH=$PATH:$CHECKM:$GTDBTK
######################################
######################################
# Add anonymous access # Add anonymous access
ADD irods /root/.irods ADD irods /root/.irods
......
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