Refactor docker builds using bioconda.

Dockerfile

@@ -1,85 +1,7 @@
-# openjdk:8 moved from debian jessie to stretch after u131, which breaks everything (bowtie)
-FROM openjdk:8u121
+FROM continuumio/miniconda
+LABEL authors="[email protected]" \
+    description="Docker image containing all requirements for the nf-core/MethylSeq pipeline"
 
-LABEL authors="[email protected],[email protected]" \
-    description="Docker image containing all requirements for nf-core/MethylSeq pipeline"
-
-# 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++ \
-        gcc \
-        gfortran \
-        libbz2-dev \
-        libcurl4-openssl-dev \
-        libgsl0-dev \
-        liblzma-dev \
-        libncurses5-dev \
-        libpcre3-dev \
-        libreadline-dev \
-        libssl-dev \
-        libtbb-dev \
-        make \
-        python-dev \
-        zlib1g-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-# 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
-
-RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -o /opt/fastqc_v0.11.5.zip && \
-    unzip /opt/fastqc_v0.11.5.zip -d /opt/ && \
-    chmod 755 /opt/FastQC/fastqc && \
-    ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
-    rm /opt/fastqc_v0.11.5.zip
-
-# Install cutadapt
-RUN pip install cutadapt
-
-# Install TrimGalore
-RUN mkdir /opt/TrimGalore && \
-    curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.zip -o /opt/TrimGalore/0.4.4.zip && \
-    unzip /opt/TrimGalore/0.4.4.zip -d /opt/TrimGalore && \
-    ln -s /opt/TrimGalore/TrimGalore-0.4.4/trim_galore /usr/local/bin/trim_galore && \
-    rm /opt/TrimGalore/0.4.4.zip
-
-# Install SAMTools
-RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2 -o /opt/samtools-1.5.tar.bz2 && \
-    tar xvjf /opt/samtools-1.5.tar.bz2 -C /opt/ && \
-    cd /opt/samtools-1.5 && \
-    make && \
-    make install && \
-    rm /opt/samtools-1.5.tar.bz2
-
-# Install Bowtie2
-RUN mkdir /opt/bowtie2 && \
-    curl -fsSL https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.2/bowtie2-2.3.2-source.zip -o /opt/bowtie2/bowtie2.zip && \
-    unzip /opt/bowtie2/bowtie2.zip -d /opt/bowtie2 && \
-    cd /opt/bowtie2/bowtie2-2.3.2/ && \
-    make && \
-    ln -s /opt/bowtie2/bowtie2-2.3.2/bowtie2 /usr/local/bin/bowtie2 && \
-    ln -s /opt/bowtie2/bowtie2-2.3.2/bowtie2-build /usr/local/bin/bowtie2-build && \
-    rm /opt/bowtie2/bowtie2.zip
-
-# Install Bismark
-RUN mkdir /opt/Bismark && \
-    curl -fsSL https://github.com/FelixKrueger/Bismark/archive/0.18.2.zip -o /opt/Bismark/bismark.zip && \
-    unzip /opt/Bismark/bismark.zip -d /opt/Bismark && \
-    rm /opt/Bismark/bismark.zip
-ENV PATH="/opt/Bismark/Bismark-0.18.2:${PATH}"
-
-# Install Qualimap
-RUN mkdir /opt/Qualimap && \
-    curl -fsSL https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip -o /opt/Qualimap/qualimap.zip && \
-    unzip /opt/Qualimap/qualimap.zip -d /opt/Qualimap && \
-    ln -s /opt/Qualimap/qualimap_v2.2.1/qualimap /usr/local/bin/qualimap && \
-    rm /opt/Qualimap/qualimap.zip
-
-# Install MultiQC
-RUN pip install git+https://github.com/ewels/MultiQC.git
-
-# Create root directories for UPPMAX and c3se hebbe
-RUN mkdir /pica /lupus /crex1 /crex2 /proj /scratch /sw \
-          /c3se /local /apps
+COPY environment.yml /
+RUN conda env create -f /environment.yml
+ENV PATH /opt/conda/envs/nfcore-methylseq/bin:$PATH

environment.yml

@@ -0,0 +1,17 @@
+name: nfcore-methylseq
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # Default bismark
+  - fastqc=0.11.5
+  - trim-galore=0.4.5
+  - samtools=1.7
+  - bowtie2=2.3.4.1
+  - bismark=0.19.0
+  - qualimap=2.2.2a
+  - multiqc=1.4
+  # bwa-meth aligner
+  - picard=2.17.8
+  - bwameth=0.2.0
+  - methyldackel=0.3.0

nextflow.config

@@ -105,6 +105,7 @@ manifest {
   homePage = 'https://github.com/nf-core/MethylSeq'
   description = 'Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.'
   mainScript = 'bismark.nf'
+  foo = 'bar'
 }
 
 // Function to ensure that resource requirements don't go beyond