nf-core · ewels · Apr 24, 2018 · Apr 24, 2018
diff --git a/Dockerfile b/Dockerfile
@@ -1,154 +1,8 @@
-FROM openjdk:8
-
-LABEL author="Phil Ewels" \
-    description="Docker image containing all requirements for nf-core/ChIPseq pipeline" \
-    maintainer="[email protected]"
-
-# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-        g++ \
-        gawk \
-        gcc \
-        gfortran \
-        libboost-all-dev \
-        libbz2-dev \
-        libcurl4-openssl-dev \
-        libdbd-mysql \
-        libgsl0-dev \
-        liblzma-dev \
-        libmariadb-client-lgpl-dev \
-        libncurses5-dev \
-        libpcre3-dev \
-        libreadline-dev \
-        libssl-dev \
-        libxml2-dev \
-        make \
-        python-dev \
-        zlib1g-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-# Use gawk instead of awk (needed for phantompeakqualtools)
-RUN update-alternatives --set awk /usr/bin/gawk
-
-# Install pip
-RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \
-    python /opt/get-pip.py && \
-    rm /opt/get-pip.py
-
-# Install FastQC
-ENV FASTQC_BIN="fastqc_v0.11.5.zip"
-RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/$FASTQC_BIN -o /opt/$FASTQC_BIN && \
-    unzip /opt/$FASTQC_BIN -d /opt/ && \
-    chmod 755 /opt/FastQC/fastqc && \
-    ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
-    rm /opt/$FASTQC_BIN
-
-# Install cutadapt
-RUN pip install cutadapt
-
-# Install TrimGalore
-ENV TRIMGALORE_VERSION="0.4.5"
-RUN curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/${TRIMGALORE_VERSION}.tar.gz -o /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz && \
-    tar xvzf /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz -C /opt/ && \
-    ln -s /opt/TrimGalore-${TRIMGALORE_VERSION}/trim_galore /usr/local/bin/trim_galore && \
-    rm /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz
-
-# Install BWA
-ENV BWA_VERSION="0.7.15"
-RUN curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-${BWA_VERSION}.tar.bz2 -o /opt/bwa-${BWA_VERSION}.tar.bz2 && \
-    tar xvjf /opt/bwa-${BWA_VERSION}.tar.bz2 -C /opt/ && \
-    cd /opt/bwa-${BWA_VERSION};make && \
-    ln -s /opt/bwa-${BWA_VERSION}/bwa /usr/local/bin/bwa && \
-    rm /opt/bwa-${BWA_VERSION}.tar.bz2
-
-# Install SAMTools
-ENV SAMTOOLS_VERSON="1.6"
-RUN curl -fsSL https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSON}/samtools-${SAMTOOLS_VERSON}.tar.bz2 -o /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 && \
-    tar xvjf /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 -C /opt/ && \
-    cd /opt/samtools-${SAMTOOLS_VERSON};make;make install && \
-    rm /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2
-
-# Install PicardTools
-ENV PICARD_VERSION="picard-tools-2.0.1"
-RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/${PICARD_VERSION}.zip -o /opt/${PICARD_VERSION}.zip && \
-    unzip /opt/${PICARD_VERSION}.zip -d /opt/ && \
-    rm /opt/${PICARD_VERSION}.zip
-ENV PICARD_HOME /opt/${PICARD_VERSION}
-
-# Install BEDTools
-ENV BEDTOOLS_VERSION="bedtools-2.26.0"
-RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v2.26.0/${BEDTOOLS_VERSION}.tar.gz -o /opt/${BEDTOOLS_VERSION}.tar.gz && \
-    tar xvzf /opt/${BEDTOOLS_VERSION}.tar.gz -C /opt/ && \
-    cd /opt/bedtools2; make && \
-    cp /opt/bedtools2/bin/* /usr/local/bin/ && \
-    rm /opt/${BEDTOOLS_VERSION}.tar.gz
-
-# Install R
-ENV R_VERSION="R-3.4.2"
-RUN curl -fsSL https://cran.r-project.org/src/base/R-3/${R_VERSION}.tar.gz -o /opt/${R_VERSION}.tar.gz && \
-    tar xvzf /opt/${R_VERSION}.tar.gz -C /opt/ && \
-    cd /opt/${R_VERSION};./configure;make;make install && \
-    rm /opt/${R_VERSION}.tar.gz
-
-# Install core R dependencies
-RUN echo "r <- getOption('repos'); r['CRAN'] <- 'https://ftp.acc.umu.se/mirror/CRAN/'; options(repos = r);" > ~/.Rprofile && \
-    Rscript -e "install.packages('caTools',dependencies=TRUE)" && \
-    Rscript -e "install.packages('snow',dependencies=TRUE)" && \
-    Rscript -e "install.packages('doMC',dependencies=TRUE)" && \
-    Rscript -e "install.packages('utils',dependencies=TRUE)" && \
-    Rscript -e "install.packages('stringr',dependencies=TRUE)" && \
-    Rscript -e "install.packages('markdown',dependencies=TRUE)" && \
-    Rscript -e "install.packages('evaluate',dependencies=TRUE)" && \
-    Rscript -e "install.packages('ggplot2',dependencies=TRUE)" && \
-    Rscript -e "install.packages('knitr',dependencies=TRUE)" && \
-    Rscript -e "install.packages('RMySQL',dependencies=TRUE)"
-
-# Install R Bioconductor packages
-RUN echo 'source("https://bioconductor.org/biocLite.R")' > /opt/packages.r && \
-    echo 'biocLite()' >> /opt/packages.r && \
-    echo 'biocLite(c("BSgenome", "Rsamtools", "ShortRead", "GenomicRanges", "GenomicFeatures", "ensembldb", "ChIPpeakAnno", "biomaRt", "rtracklayer", "BSgenome.Hsapiens.UCSC.hg19", "org.Hs.eg.db", "BSgenome.Mmusculus.UCSC.mm10", "org.Mm.eg.db"))' >> /opt/packages.r && \
-    Rscript /opt/packages.r && \
-    mkdir /usr/local/lib/R/site-library
-
-# Install phantompeakqualtools
-ENV SPP_VERSION="1.15"
-ENV PHANTOMPEAKQUALTOOLS_VERSION="v.1.1"
-RUN curl -fsSL https://github.com/hms-dbmi/spp/archive/${SPP_VERSION}.tar.gz -o /opt/SPP_${SPP_VERSION}.tar.gz && \
-    Rscript -e "install.packages('/opt/SPP_${SPP_VERSION}.tar.gz',dependencies=TRUE)" && \
-    rm /opt/SPP_${SPP_VERSION}.tar.gz && \
-    curl -fsSL https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/phantompeakqualtools/ccQualityControl.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz -o /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz && \
-    tar xvzf /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz -C /opt/ && \
-    chmod 755 /opt/phantompeakqualtools/* && \
-    echo 'alias run_spp.R="Rscript /opt/phantompeakqualtools/run_spp.R"' >> ~/.bashrc && \
-    rm /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz
-ENV PATH=${PATH}:/opt/phantompeakqualtools
-
-# Install DeepTools
-ENV DEEPTOOLS_VERSION="2.5.4"
-RUN pip install git+git://github.com/fidelram/deepTools.git@$DEEPTOOLS_VERSION
-
-# Install ngsplot
-ENV NGSPLOT_VERSION="2.63"
-RUN curl -fsSL https://github.com/shenlab-sinai/ngsplot/archive/${NGSPLOT_VERSION}.tar.gz -o /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz && \
-    tar xvzf /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz -C /opt/ && \
-    rm /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz
-ENV PATH=${PATH}:/opt/ngsplot-${NGSPLOT_VERSION}/bin
-ENV NGSPLOT=/opt/ngsplot-${NGSPLOT_VERSION}/
-RUN curl -fsSL https://export.uppmax.uu.se/b2013064/test-data/nfcore-chipseq_test_set.tar.bz2 -o /opt/nfcore-chipseq_test_set.tar.bz2 && \
-    tar xvjf /opt/nfcore-chipseq_test_set.tar.bz2 -C /opt/ && \
-    echo y | ngsplotdb.py install /opt/nfcore-chipseq_test_set/ngsplotdb_mm10_75_3.00.tar.gz && \
-    echo y | ngsplotdb.py install /opt/nfcore-chipseq_test_set/ngsplotdb_hg19_75_3.00.tar.gz && \
-    rm /opt/nfcore-chipseq_test_set.tar.bz2 && \
-    rm -rf /opt/nfcore-chipseq_test_set
-
-# Install MACS
-RUN pip install MACS2
-
-# Install MultiQC
-ENV MULTIQC_VERSION="v1.4"
-RUN pip install git+git://github.com/ewels/MultiQC.git@$MULTIQC_VERSION
-
-# Create root directories for UPPMAX and c3se hebbe
-RUN mkdir /pica /lupus /crex1 /crex2 /proj /scratch /sw \
-          /c3se /local /apps
+FROM nfcore/base
+MAINTAINER Phil Ewels <[email protected]>
+LABEL authors="[email protected]" \
+    description="Docker image containing all requirements for the nfcore/ChIPseq pipeline"
+
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nfcore-chipseq-1.4dev/bin:$PATH
diff --git a/Dockerfile_manual b/Dockerfile_manual
@@ -0,0 +1,150 @@
+FROM openjdk:8
+
+LABEL author="Phil Ewels" \
+    description="Docker image containing all requirements for nf-core/ChIPseq pipeline" \
+    maintainer="[email protected]"
+
+# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        g++ \
+        gawk \
+        gcc \
+        gfortran \
+        libboost-all-dev \
+        libbz2-dev \
+        libcurl4-openssl-dev \
+        libdbd-mysql \
+        libgsl0-dev \
+        liblzma-dev \
+        libmariadb-client-lgpl-dev \
+        libncurses5-dev \
+        libpcre3-dev \
+        libreadline-dev \
+        libssl-dev \
+        libxml2-dev \
+        make \
+        python-dev \
+        zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Use gawk instead of awk (needed for phantompeakqualtools)
+RUN update-alternatives --set awk /usr/bin/gawk
+
+# Install pip
+RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \
+    python /opt/get-pip.py && \
+    rm /opt/get-pip.py
+
+# Install FastQC
+ENV FASTQC_BIN="fastqc_v0.11.5.zip"
+RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/$FASTQC_BIN -o /opt/$FASTQC_BIN && \
+    unzip /opt/$FASTQC_BIN -d /opt/ && \
+    chmod 755 /opt/FastQC/fastqc && \
+    ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
+    rm /opt/$FASTQC_BIN
+
+# Install cutadapt
+RUN pip install cutadapt
+
+# Install TrimGalore
+ENV TRIMGALORE_VERSION="0.4.5"
+RUN curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/${TRIMGALORE_VERSION}.tar.gz -o /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz && \
+    tar xvzf /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz -C /opt/ && \
+    ln -s /opt/TrimGalore-${TRIMGALORE_VERSION}/trim_galore /usr/local/bin/trim_galore && \
+    rm /opt/trimgalore_${TRIMGALORE_VERSION}.tar.gz
+
+# Install BWA
+ENV BWA_VERSION="0.7.15"
+RUN curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-${BWA_VERSION}.tar.bz2 -o /opt/bwa-${BWA_VERSION}.tar.bz2 && \
+    tar xvjf /opt/bwa-${BWA_VERSION}.tar.bz2 -C /opt/ && \
+    cd /opt/bwa-${BWA_VERSION};make && \
+    ln -s /opt/bwa-${BWA_VERSION}/bwa /usr/local/bin/bwa && \
+    rm /opt/bwa-${BWA_VERSION}.tar.bz2
+
+# Install SAMTools
+ENV SAMTOOLS_VERSON="1.6"
+RUN curl -fsSL https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSON}/samtools-${SAMTOOLS_VERSON}.tar.bz2 -o /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 && \
+    tar xvjf /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2 -C /opt/ && \
+    cd /opt/samtools-${SAMTOOLS_VERSON};make;make install && \
+    rm /opt/samtools-${SAMTOOLS_VERSON}.tar.bz2
+
+# Install PicardTools
+ENV PICARD_VERSION="picard-tools-2.0.1"
+RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/${PICARD_VERSION}.zip -o /opt/${PICARD_VERSION}.zip && \
+    unzip /opt/${PICARD_VERSION}.zip -d /opt/ && \
+    rm /opt/${PICARD_VERSION}.zip
+ENV PICARD_HOME /opt/${PICARD_VERSION}
+
+# Install BEDTools
+ENV BEDTOOLS_VERSION="bedtools-2.26.0"
+RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v2.26.0/${BEDTOOLS_VERSION}.tar.gz -o /opt/${BEDTOOLS_VERSION}.tar.gz && \
+    tar xvzf /opt/${BEDTOOLS_VERSION}.tar.gz -C /opt/ && \
+    cd /opt/bedtools2; make && \
+    cp /opt/bedtools2/bin/* /usr/local/bin/ && \
+    rm /opt/${BEDTOOLS_VERSION}.tar.gz
+
+# Install R
+ENV R_VERSION="R-3.4.2"
+RUN curl -fsSL https://cran.r-project.org/src/base/R-3/${R_VERSION}.tar.gz -o /opt/${R_VERSION}.tar.gz && \
+    tar xvzf /opt/${R_VERSION}.tar.gz -C /opt/ && \
+    cd /opt/${R_VERSION};./configure;make;make install && \
+    rm /opt/${R_VERSION}.tar.gz
+
+# Install core R dependencies
+RUN echo "r <- getOption('repos'); r['CRAN'] <- 'https://ftp.acc.umu.se/mirror/CRAN/'; options(repos = r);" > ~/.Rprofile && \
+    Rscript -e "install.packages('caTools',dependencies=TRUE)" && \
+    Rscript -e "install.packages('snow',dependencies=TRUE)" && \
+    Rscript -e "install.packages('doMC',dependencies=TRUE)" && \
+    Rscript -e "install.packages('utils',dependencies=TRUE)" && \
+    Rscript -e "install.packages('stringr',dependencies=TRUE)" && \
+    Rscript -e "install.packages('markdown',dependencies=TRUE)" && \
+    Rscript -e "install.packages('evaluate',dependencies=TRUE)" && \
+    Rscript -e "install.packages('ggplot2',dependencies=TRUE)" && \
+    Rscript -e "install.packages('knitr',dependencies=TRUE)" && \
+    Rscript -e "install.packages('RMySQL',dependencies=TRUE)"
+
+# Install R Bioconductor packages
+RUN echo 'source("https://bioconductor.org/biocLite.R")' > /opt/packages.r && \
+    echo 'biocLite()' >> /opt/packages.r && \
+    echo 'biocLite(c("BSgenome", "Rsamtools", "ShortRead", "GenomicRanges", "GenomicFeatures", "ensembldb", "ChIPpeakAnno", "biomaRt", "rtracklayer", "BSgenome.Hsapiens.UCSC.hg19", "org.Hs.eg.db", "BSgenome.Mmusculus.UCSC.mm10", "org.Mm.eg.db"))' >> /opt/packages.r && \
+    Rscript /opt/packages.r && \
+    mkdir /usr/local/lib/R/site-library
+
+# Install phantompeakqualtools
+ENV SPP_VERSION="1.15"
+ENV PHANTOMPEAKQUALTOOLS_VERSION="v.1.1"
+RUN curl -fsSL https://github.com/hms-dbmi/spp/archive/${SPP_VERSION}.tar.gz -o /opt/SPP_${SPP_VERSION}.tar.gz && \
+    Rscript -e "install.packages('/opt/SPP_${SPP_VERSION}.tar.gz',dependencies=TRUE)" && \
+    rm /opt/SPP_${SPP_VERSION}.tar.gz && \
+    curl -fsSL https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/phantompeakqualtools/ccQualityControl.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz -o /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz && \
+    tar xvzf /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz -C /opt/ && \
+    chmod 755 /opt/phantompeakqualtools/* && \
+    echo 'alias run_spp.R="Rscript /opt/phantompeakqualtools/run_spp.R"' >> ~/.bashrc && \
+    rm /opt/phantompeakqualtools.${PHANTOMPEAKQUALTOOLS_VERSION}.tar.gz
+ENV PATH=${PATH}:/opt/phantompeakqualtools
+
+# Install DeepTools
+ENV DEEPTOOLS_VERSION="2.5.4"
+RUN pip install git+git://github.com/fidelram/deepTools.git@$DEEPTOOLS_VERSION
+
+# Install ngsplot
+ENV NGSPLOT_VERSION="2.63"
+RUN curl -fsSL https://github.com/shenlab-sinai/ngsplot/archive/${NGSPLOT_VERSION}.tar.gz -o /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz && \
+    tar xvzf /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz -C /opt/ && \
+    rm /opt/ngsplot_${NGSPLOT_VERSION}.tar.gz
+ENV PATH=${PATH}:/opt/ngsplot-${NGSPLOT_VERSION}/bin
+ENV NGSPLOT=/opt/ngsplot-${NGSPLOT_VERSION}/
+RUN curl -fsSL https://export.uppmax.uu.se/b2013064/test-data/nfcore-chipseq_test_set.tar.bz2 -o /opt/nfcore-chipseq_test_set.tar.bz2 && \
+    tar xvjf /opt/nfcore-chipseq_test_set.tar.bz2 -C /opt/ && \
+    echo y | ngsplotdb.py install /opt/nfcore-chipseq_test_set/ngsplotdb_mm10_75_3.00.tar.gz && \
+    echo y | ngsplotdb.py install /opt/nfcore-chipseq_test_set/ngsplotdb_hg19_75_3.00.tar.gz && \
+    rm /opt/nfcore-chipseq_test_set.tar.bz2 && \
+    rm -rf /opt/nfcore-chipseq_test_set
+
+# Install MACS
+RUN pip install MACS2
+
+# Install MultiQC
+ENV MULTIQC_VERSION="v1.4"
+RUN pip install git+git://github.com/ewels/MultiQC.git@$MULTIQC_VERSION
diff --git a/README.md b/README.md
@@ -4,6 +4,7 @@
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)
 [![Gitter](https://img.shields.io/badge/gitter-%20join%20chat%20%E2%86%92-4fb99a.svg)](https://gitter.im/nf-core/Lobby)
 
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker Container available](https://img.shields.io/docker/automated/nfcore/chipseq.svg)](https://hub.docker.com/r/nfcore/chipseq/)
 ![Singularity Container available](
 https://img.shields.io/badge/singularity-available-7E4C74.svg)

diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,46 @@
+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: nfcore-chipseq-1.4dev
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - conda-forge::openjdk=8.0.144 # Needed for FastQC - conda build hangs without this
+  - fastqc=0.11.7
+  - trim-galore=0.4.5
+  - bwa=0.7.17
+  - conda-forge::r-markdown=0.8
+  - bioconda::r-spp=1.15.2
+  - bedtools=2.27.1
+  - samtools=1.8
+  - picard=2.18.2
+  - deeptools=3.0.2
+  - macs2=2.1.1
+  - multiqc=1.5
+
+# TODO:
+# - phantompeakqualtools
+# - R: caTools
+# - R: snow
+# - R: doMC
+# - R: utils
+# - R: stringr
+# - R: markdown
+# - R: evaluate
+# - R: ggplot2
+# - R: knitr
+# - R: RMySQL
+# - Bioconductor: BSgenome
+# - Bioconductor: Rsamtools
+# - Bioconductor: ShortRead
+# - Bioconductor: GenomicRanges
+# - Bioconductor: GenomicFeatures
+# - Bioconductor: ensembldb
+# - Bioconductor: ChIPpeakAnno
+# - Bioconductor: biomaRt
+# - Bioconductor: rtracklayer
+# - Bioconductor: BSgenome.Hsapiens.UCSC.hg19
+# - Bioconductor: org.Hs.eg.db
+# - Bioconductor: BSgenome.Mmusculus.UCSC.mm10
+# - Bioconductor: org.Mm.eg.db