cleanup and added gtdbtk

Dockerfile

@@ -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
 
-# Install the CWL runner (cwltool)
-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 && \
-	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
+# Some default needed stuff
+RUN apt-get update && apt-get install -y git build-essential curl wget nano htop pigz zip unzip
 
-# Install Java via sdkman
-RUN apt-get update
-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 && \
+# Install the CWL runner (cwltool) and python and pip
+RUN apt-get update && apt-get install -y nodejs cpanminus python3 python3-dev python3-distutils && \
 	curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py && \
 	pip3 install cwltool &&\
 	cwltool --version && pip install html5lib
@@ -79,13 +34,13 @@ RUN pip install python-irodsclient --upgrade && \
 	apt-get update && apt-get install -y irods-icommands
 
 # Install Java via sdkman
-RUN apt-get update
-RUN apt-get -qq -y install \
-    curl \
-    unzip \
-    zip
+# RUN apt-get update
+# 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 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" &&\
@@ -95,25 +50,39 @@ RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\
 
 # Other packages
 # 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 && \
 	add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/' && \
 	apt update && \
 	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
 # 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
-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/
+## CheckM
 RUN pip3 install pysam numpy matplotlib checkm-genome && \
 	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 irods /root/.irods