Update Dockerfile and tool versions

.github/workflows/ci.yml

@@ -13,8 +13,6 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    env:
-      IMAGE_HASH: f912436e8791a9d1f9cadf76099f760151435a43d7873712ee692cb2b0f8947e
     steps:
     - uses: actions/checkout@v2
     - name: Set up JDK 1.8
@@ -24,10 +22,6 @@ jobs:
     - name: Set up Nextflow
       run: |
         curl -fsSL get.nextflow.io | bash -e
-
-    - name: Fetch Docker image
-      run: |
-        docker pull ${{ github.repository }}@sha256:$IMAGE_HASH
     - name: Run pipeline
       run: |
         .github/workflows/ci.sh run -with-docker

chipseq-pipeline.nf

@@ -224,7 +224,7 @@ process mapping {
                   - \
   | samtools sort -@ ${cpus} \
                   - \
-                  ${prefix}_primary
+                  -o ${prefix}_primary.bam
   """
 }
 // Merge or rename bam

docker/Dockerfile

@@ -1,60 +1,129 @@
-FROM grape/mapping:gem-1.7.1
+ARG UBUNTU_VERSION=20.04
+FROM ubuntu:${UBUNTU_VERSION} as builder
 
-LABEL maintainer "Emilio Palumbo <[email protected]>" \
-      version "1.0" \
-      description "ChIP-seq analysis pipeline image"
+# install needed tools
+RUN apt-get update \
+    &&  DEBIAN_FRONTEND=noninteractve apt-get install -y --no-install-recommends \
+         ca-certificates \
+         curl \
+         gdebi-core \
+         git \
+         libboost-all-dev \
+         libcurl4-gnutls-dev \
+         libxml2-dev \
+         lsb-release \
+        #  ncurses-dev \
+         python3-dev \
+         python3-pip \
+         python-is-python3
 
-ENV _ZERONE_VERSION 5af03a1
+# install R
+ARG R_VER=3.6.3
+RUN export UBUNTU_VER=$(lsb_release -rs | tr -d '.') \
+    && curl -O https://cdn.rstudio.com/r/ubuntu-${UBUNTU_VER}/pkgs/r-${R_VER}_1_amd64.deb \
+    && DEBIAN_FRONTEND=noninteractve gdebi --non-interactive r-${R_VER}_1_amd64.deb
 
-ENV PATH=/phantompeakqualtools/:$PATH
+ENV PATH=/opt/R/${R_VER}/bin:$PATH
 
-# install needed tools
-RUN apt-get update --fix-missing -qq && apt-get install -y -q \
-  r-base \
-  git \ 
-  libboost-dev \
-  python-dev \
-  bc \
-  && apt-get clean \
-  && apt-get purge \
-  && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-# install spp  
+RUN echo 'options(repos = "https://cloud.r-project.org/")' > ~/.Rprofile
+
+# install spp
+ARG BIOC_VER="3.10"
 RUN git clone https://github.com/kundajelab/phantompeakqualtools \
   && cd phantompeakqualtools/ \
-  && R -e 'install.packages( c("snow","snowfall","bitops","caTools"), repos="http://cran.us.r-project.org"); \
-    source("http://bioconductor.org/biocLite.R"); \
-    biocLite("Rsamtools",suppressUpdates=TRUE); \
-    install.packages("./spp_1.14.tar.gz");'
+  && R -e 'install.packages( c("snow","snowfall","bitops","caTools", "BiocManager")); \
+    BiocManager::install(version = "'$BIOC_VER'"); \
+    BiocManager::install("Rsamtools", ask=FALSE); \
+    install.packages("spp");'
 
 # install Macs2
-RUN pip install numpy \ 
-    && pip install macs2
+# ARG MACS2_VER=2.1.1.20160309
+ARG MACS2_VER=2.2.4
+RUN pip3 install numpy \
+    && pip3 install macs2==${MACS2_VER}
 
 # get KentUtils
-RUN curl -fsSLo /usr/local/bin/bedGraphToBigWig https://github.com/ENCODE-DCC/kentUtils/raw/v302.1.0/bin/linux.x86_64/bedGraphToBigWig \
-  && chmod +x /usr/local/bin/bedGraphToBigWig
-RUN curl -fsSLo /usr/local/bin/bedClip https://github.com/ENCODE-DCC/kentUtils/raw/v302.1.0/bin/linux.x86_64/bedClip \
-  && chmod +x /usr/local/bin/bedClip 
+RUN curl -fsSLO https://github.com/ENCODE-DCC/kentUtils/raw/v302.1.0/bin/linux.x86_64/bedGraphToBigWig \
+  && chmod +x bedGraphToBigWig
+RUN curl -fsSLO https://github.com/ENCODE-DCC/kentUtils/raw/v302.1.0/bin/linux.x86_64/bedClip \
+  && chmod +x bedClip
 
 # install bedtools
-RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz | tar xz \
+ARG BEDTOOLS_VER=2.26.0
+RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VER}/bedtools-${BEDTOOLS_VER}.tar.gz | tar xz \
   && cd bedtools2 \
-  && make \
-  && make install
-
-# install java
-RUN curl --header "Cookie: oraclelicense=accept-securebackup-cookie" -L http://download.oracle.com/otn-pub/java/jdk/8u121-b13/e9e7ea248e2c4826b92b3f075a80e441/jre-8u121-linux-x64.tar.gz | tar xz \
-  && update-alternatives --install /usr/bin/java java /jre1.8.0_121/bin/java 100
+  && make
 
 # install picard
-RUN curl -L -o /usr/local/bin/picard.jar https://github.com/broadinstitute/picard/releases/download/2.8.3/picard.jar \
-  && chmod +x /usr/local/bin/picard.jar
+ARG PICARD_VER=2.8.3
+RUN curl -fsSLO https://github.com/broadinstitute/picard/releases/download/${PICARD_VER}/picard.jar \
+  && chmod +x picard.jar
 
 # install zerone
+ARG ZERONE_VERSION=5af03a1
 RUN mkdir -p zerone && \
-    curl -fsSL https://github.com/nanakiksc/zerone/archive/${_ZERONE_VERSION}.tar.gz | tar xz --strip-components 1 -C zerone && \
-    make -C zerone && \
-    mv zerone/zerone /usr/local/bin && \
-    make clean -C zerone
+    curl -fsSL https://github.com/nanakiksc/zerone/archive/${ZERONE_VERSION}.tar.gz | tar xz --strip-components 1 -C zerone && \
+    make -C zerone
+
+RUN apt-get install -y --no-install-recommends ncurses-dev
+
+# install samtools
+ARG SAMTOOLS_VER=1.11
+RUN curl -fsSL https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2 \
+    | tar xj && cd samtools-${SAMTOOLS_VER} \
+    && make
+
+# install GEM
+RUN curl http://barnaserver.com/gemtools/releases/GEMTools-static-i3-1.7.1.tar.gz \
+    | tar xz
+
+RUN curl -O http://ppa.launchpad.net/linuxuprising/libpng12/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1.1+1~ppa0~focal_amd64.deb
+
+FROM ubuntu:${UBUNTU_VERSION}
+
+LABEL maintainer "Emilio Palumbo <[email protected]>" \
+      version "1.0" \
+      description "ChIP-seq analysis pipeline image"
+
+# install needed tools
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        gawk \
+        libblas3 \
+        libgomp1 \
+        libicu66 \
+        liblapack3 \
+        libcurl3-gnutls \
+        locales \
+        python-is-python3 \
+        openjdk-8-jre-headless
+
+# set locale
+RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
+    && locale-gen en_US.utf8 \
+    && /usr/sbin/update-locale LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
+
+# set environment variables
+ARG R_VER=3.6.3
+ENV LANG=en_US.UTF-8 \
+    LC_ALL=en_US.UTF-8 \
+    PATH=/opt/R/${R_VER}/bin:$PATH
+
+ARG SAMTOOLS_VER=1.11
+
+COPY --from=builder /libpng12-0_1.2.54-1ubuntu1.1+1~ppa0~focal_amd64.deb /
+RUN dpkg -i /libpng12-0_1.2.54-1ubuntu1.1+1~ppa0~focal_amd64.deb && \
+    rm libpng12-0_1.2.54-1ubuntu1.1+1~ppa0~focal_amd64.deb
 
+# Copy installed libraries from builder
+COPY --from=builder /opt/R /opt/R
+COPY --from=builder /usr/local/lib/python3.8/dist-packages /usr/local/lib/python3.8/dist-packages
+COPY --from=builder /bedtools2/bin/ /usr/local/bin/
+COPY --from=builder /bedClip /usr/local/bin
+COPY --from=builder /bedGraphToBigWig /usr/local/bin/
+COPY --from=builder /zerone/zerone /usr/local/bin/
+COPY --from=builder /picard.jar /usr/local/bin/
+COPY --from=builder /phantompeakqualtools/run_spp.R /usr/local/bin
+COPY --from=builder /gemtools-1.7.1-i3/bin/gem-* /usr/local/bin/
+COPY --from=builder /samtools-${SAMTOOLS_VER}/samtools /usr/local/bin/
+COPY --from=builder /usr/local/bin/macs2 /usr/local/bin/

nextflow.config

@@ -13,6 +13,6 @@ trace.enabled = true
 
 // Process configuration
 process {
-  container = 'guigolab/chip-nf@sha256:f912436e8791a9d1f9cadf76099f760151435a43d7873712ee692cb2b0f8947e'
+  container = 'guigolab/chip-nf:dev'
   tag = { prefix ?: genome.baseName }
 }