fix: ascatngs container

.github/workflows/docker_build_push.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
     steps:
       - name: Git checkout
         id: git_checkout

.github/workflows/docker_build_push_release.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
     steps:
       - name: Git checkout
         id: git_checkout

.github/workflows/docker_build_test_pull_request.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
     steps:
       - name: Git checkout
         id: git_checkout

BALSAMIC/containers/ascatNgs/Dockerfile

@@ -0,0 +1,183 @@
+FROM quay.io/wtsicgp/pcap-core:5.4.2 AS builder
+
+USER root
+
+ENV VER_CGPVCF="v2.2.1"
+ENV VER_VCFTOOLS="0.1.16"
+ENV VER_ALLELECOUNT="v4.2.1"
+
+RUN apt-get -yq update
+RUN apt-get install -qy --no-install-recommends lsb-release
+RUN apt-get install -qy --no-install-recommends gnupg
+RUN apt-get install -yq --no-install-recommends dirmngr
+RUN apt-get install -yq --no-install-recommends wget
+RUN apt-get install -yq --no-install-recommends build-essential
+RUN apt-get install -yq --no-install-recommends ca-certificates
+RUN apt-get install -yq --no-install-recommends locales
+RUN apt-get install -yq --no-install-recommends g++
+RUN apt-get install -yq --no-install-recommends make
+RUN apt-get install -yq --no-install-recommends gcc
+RUN apt-get install -yq --no-install-recommends git
+
+ENV DEBIAN_FRONTEND "noninteractive"
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends software-properties-common
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends locales
+RUN apt-get install -yq --no-install-recommends g++
+RUN apt-get install -yq --no-install-recommends make
+RUN apt-get install -yq --no-install-recommends gcc
+RUN apt-get install -yq --no-install-recommends wget
+RUN apt-get install -yq --no-install-recommends pkg-config
+RUN apt-get install -yq --no-install-recommends zlib1g-dev
+RUN apt-get install -yq --no-install-recommends libbz2-dev
+RUN apt-get install -yq --no-install-recommends unzip
+RUN apt-get install -yq --no-install-recommends libpng-dev
+RUN apt-get install -yq --no-install-recommends tzdata
+RUN apt-get install -yq --no-install-recommends libcurl4-openssl-dev
+RUN apt-get install -yq --no-install-recommends libxml2-dev
+RUN apt-get install -yq --no-install-recommends libgit2-dev
+RUN apt-get install -yq --no-install-recommends liblzma-dev
+RUN apt-get install -yq --no-install-recommends libssl-dev
+RUN apt-get install -yq --no-install-recommends nettle-dev
+RUN apt-get install -yq --no-install-recommends time
+RUN apt-get install -yq --no-install-recommends libcairo2-dev
+RUN apt-get install -yq --no-install-recommends gfortran
+RUN apt-get install -yq --no-install-recommends libblas-dev
+RUN apt-get install -yq --no-install-recommends libboost-all-dev
+RUN apt-get install -yq --no-install-recommends libpstreams-dev
+RUN apt-get install -yq --no-install-recommends cpanminus
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$PATH
+ENV PERL5LIB $OPT/lib/perl5
+ENV LD_LIBRARY_PATH $OPT/lib
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV R_LIBS $OPT/R-libs
+ENV R_LIBS_USER $R_LIBS
+ENV R_PROFILE_USER $OPT/config/Rprofile
+RUN mkdir -p $OPT
+RUN mkdir $OPT/config/
+RUN mkdir -p $R_LIBS_USER
+WORKDIR /R
+RUN cd /R && wget --progress=dot:giga -q -nv https://cdn.rstudio.com/r/ubuntu-2004/pkgs/r-4.2.1_1_amd64.deb &&\
+	apt-get install --no-install-recommends -f -y ./r-4.2.1_1_amd64.deb &&\
+	ln -s /opt/R/4.2.1/bin/R /usr/bin/R &&\
+    ln -s /opt/R/4.2.1/bin/Rscript /usr/bin/Rscript &&\
+    ln -s /opt/R/4.2.1/lib/R /usr/lib/R
+WORKDIR /git
+RUN cd /git && git clone --recursive https://github.com/cancerit/ascatNgs.git &&\
+   cd ascatNgs &&\
+   ./setup.sh $OPT
+
+USER    ubuntu
+FROM ubuntu:20.04
+
+RUN apt-get -yq update && \
+apt-get install -qy --no-install-recommends \
+lsb-release \
+gnupg \
+dirmngr \
+wget \
+build-essential \
+locales \
+gcc \
+wget \
+pkg-config \
+cpanminus \
+git \
+unattended-upgrades && \
+unattended-upgrade -d -v && \
+apt-get remove -yq unattended-upgrades && \
+apt-get autoremove -yq &&\
+apt-get clean && \
+rm -rf /var/lib/apt/lists/*
+
+ENV DEBIAN_FRONTEND "noninteractive"
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+RUN apt-get -yq update \
+&& apt-get install -yq --no-install-recommends \
+software-properties-common \
+libreadline6-dev \
+libx11-dev \
+libxt-dev \
+libpng-dev \
+libjpeg-dev \
+libcairo2-dev \
+libcairo2-dev \
+xvfb \
+libbz2-dev \
+libzstd-dev \
+liblzma-dev \
+libcurl4-openssl-dev \
+texinfo \
+texlive \
+texlive-fonts-extra \
+screen \
+libpcre2-dev \
+locales \
+curl \
+wget \
+ca-certificates \
+libperlio-gzip-perl \
+bzip2 \
+psmisc \
+time \
+zlib1g \
+liblzma5 \
+libncurses5 \
+p11-kit \
+libcurl3-gnutls \
+libcurl4 \
+moreutils \
+google-perftools \
+libcairo2 \
+gfortran \
+unattended-upgrades && \
+unattended-upgrade -d -v && \
+apt-get remove -yq unattended-upgrades && \
+apt-get autoremove -yq && \
+apt-get clean && \
+rm -rf /var/lib/apt/lists/*
+
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$PATH
+ENV PERL5LIB $OPT/lib/perl5
+ENV LD_LIBRARY_PATH $OPT/lib
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV R_LIBS $OPT/R-libs
+ENV R_LIBS_USER $R_LIBS
+ENV R_PROFILE_USER $OPT/config/Rprofile
+
+RUN mkdir -p $OPT
+COPY --from=builder $OPT $OPT
+COPY --from=builder /opt/R /opt/R
+WORKDIR /R
+RUN cd /R && wget --progress=dot:giga -q -nv https://cdn.rstudio.com/r/ubuntu-2004/pkgs/r-4.2.1_1_amd64.deb &&\
+	apt-get install --no-install-recommends -f -y ./r-4.2.1_1_amd64.deb
+RUN	ln -s /opt/R/4.2.1/bin/R /usr/bin/R
+RUN ln -s /opt/R/4.2.1/bin/Rscript /usr/bin/Rscript
+RUN ln -s /opt/R/4.2.1/lib/R /usr/lib/R
+RUN rm -rf /R
+RUN rm -rf /var/lib/apt/lists/*
+RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
+
+USER ubuntu
+WORKDIR /home/ubuntu
+
+CMD ["/bin/bash"]

CHANGELOG.rst

@@ -20,7 +20,7 @@ Fixed:
 * Bump cryptography to v40.0.2 and gsutil to v5.23 https://github.com/Clinical-Genomics/BALSAMIC/pull/1154
 * Pytest file saved in balsamic directory https://github.com/Clinical-Genomics/BALSAMIC/pull/1093
 * Fix varcall_py3 container bcftools dependency error https://github.com/Clinical-Genomics/BALSAMIC/pull/1097
-
+* AscatNgs container https://github.com/Clinical-Genomics/BALSAMIC/pull/1155
 
 [11.2.0]
 --------

container_tests/ascatNgs/ascatNgs.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+# Test if commands exist
+
+valid_commands=( "ascat.pl" "R" )
+
+for valid_command in "${valid_commands[@]}"
+do
+  if ! command -v "${valid_command}" &> /dev/null
+  then
+    echo "${valid_command} could not be found"
+    exit 1
+  else
+    echo "${valid_command} command is found and valid"
+  fi
+done
+