Merge pull request #99 from sanger-pathogens/fix_docker_build

new docker file

.travis.yml

@@ -5,6 +5,8 @@ addons:
  - zlib1g-dev
  - libncurses5-dev
  - libncursesw5-dev
+ - libbz2-dev
+ - liblzma-dev
 cache:
  directories:
  - build
@@ -33,4 +35,4 @@ before_script:
 script:
  - "coverage run setup.py test"
 after_success:
- - codecov
+ - codecov

Dockerfile

@@ -1,26 +1,101 @@
 # This container will install IVA from master
 #
-FROM debian:testing
+FROM ubuntu:18.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+WORKDIR /tmp
+
+ENV INSTALL_DIRECTORY=/opt
+
 
 # Install required dependancies
-RUN apt-get -qq update && apt-get install -y openjdk-8-jdk python3-pip git wget unzip zlib1g-dev libncurses5-dev
+RUN apt-get update -y -qq \
+ && apt-get install -y -qq \
+ openjdk-8-jdk \
+ python3-pip \
+ git \
+ wget \
+ unzip \
+ zlib1g-dev \
+ libncurses5-dev \
+ libbz2-dev \
+ liblzma-dev
+
 ENV JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64"
-RUN git clone https://github.com/sanger-pathogens/iva.git
-RUN cd iva && ./install_dependencies.sh
-ENV PATH /iva/build/kmc-2.3.0:/iva/build/samtools-1.3:/iva/build/smalt-0.7.6-bin:/iva/build/samtools-1.3:/iva/build/MUMmer3.23:/iva/build/SPAdes-3.7.1-Linux/bin:$PATH
-RUN export PATH
 
-# Install optional dependencies
-RUN wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip && unzip Trimmomatic-0.38.zip
+ARG KMC_VERSION=3.0.0
+ARG MUMMER_VERSION=3.23
+ARG SAMTOOLS_VERSION=1.3
+ARG SMALT_VERSION=0.7.6
+ARG TRIMMOMATIC_VERSION=0.38
+ARG KRAKEN_VERSION=1.0
+ARG BLAST_VERSION=2.5.0
+
+# kmc
+RUN mkdir /opt/kmc-${KMC_VERSION} \
+ && cd /opt/kmc-${KMC_VERSION} \
+ && wget --progress=dot:giga https://github.com/refresh-bio/KMC/releases/download/v${KMC_VERSION}/KMC3.linux.tar.gz \
+ && tar xf KMC3.linux.tar.gz \
+ && rm KMC3.linux.tar.gz \
+ && chmod -R 755 /opt/kmc-${KMC_VERSION}
+ENV PATH=/opt/kmc-${KMC_VERSION}:$PATH
+
+# MUMmer
+RUN cd /opt \
+ && wget --progress=dot:giga "http://downloads.sourceforge.net/project/mummer/mummer/${MUMMER_VERSION}/MUMmer${MUMMER_VERSION}.tar.gz" \
+ && tar xf MUMmer${MUMMER_VERSION}.tar.gz \
+ && rm MUMmer${MUMMER_VERSION}.tar.gz \
+ && cd MUMmer${MUMMER_VERSION} \
+ && make
+ENV PATH=/opt/MUMmer${MUMMER_VERSION}:$PATH
+
+# samtools
+RUN cd /opt \
+ && wget --progress=dot:giga "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" \
+ && tar xf samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ && rm samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ && cd samtools-${SAMTOOLS_VERSION} \
+ && make
+ENV PATH=/opt/samtools-${SAMTOOLS_VERSION}:$PATH
+
+# smalt
+RUN cd /opt \
+ && wget --progress=dot:giga http://downloads.sourceforge.net/project/smalt/smalt-${SMALT_VERSION}-bin.tar.gz \
+ && tar xf smalt-${SMALT_VERSION}-bin.tar.gz \
+ && rm smalt-${SMALT_VERSION}-bin.tar.gz \
+ && cd smalt-${SMALT_VERSION}-bin \
+ && ln -fs smalt_x86_64 smalt
+ENV PATH=/opt/smalt-${SMALT_VERSION}-bin:$PATH
+
+# Trimmomatic
+RUN cd / \
+ && wget --progress=dot:giga http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-${TRIMMOMATIC_VERSION}.zip \
+ && unzip Trimmomatic-${TRIMMOMATIC_VERSION}.zip \
+ && rm Trimmomatic-${TRIMMOMATIC_VERSION}.zip
 
-RUN wget http://ccb.jhu.edu/software/kraken/dl/kraken-1.0.tgz && tar -xvzf kraken-1.0.tgz
-RUN cd kraken-1.0 && ./install_kraken.sh ../kraken_install
-ENV PATH /kraken_install/:$PATH
-RUN export PATH
+# Kraken
+RUN mkdir /tmp/KRAKEN \
+ && cd /tmp/KRAKEN \
+ && wget --progress=dot:giga http://ccb.jhu.edu/software/kraken/dl/kraken-${KRAKEN_VERSION}.tgz \
+ && tar -xvzf kraken-${KRAKEN_VERSION}.tgz \
+ && cd kraken-${KRAKEN_VERSION} \
+ && ./install_kraken.sh /opt/kraken-${KRAKEN_VERSION} \
+ && rm -rf /tmp/KRAKEN
+ENV PATH=/opt/kraken-${KRAKEN_VERSION}/:$PATH
 
-RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.5.0/ncbi-blast-2.5.0+-x64-linux.tar.gz && tar -xzvf ncbi-blast-2.5.0+-x64-linux.tar.gz
-ENV PATH /ncbi-blast-2.5.0+:$PATH
-RUN export PATH
+# ncbi blast
+RUN cd /opt \
+ && wget --progress=dot:giga ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz \
+ && tar -xf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz \
+ && rm ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
+ENV PATH=/opt/ncbi-blast-${BLAST_VERSION}+/bin:$PATH
 
 # Install IVA
-RUN cd iva && python3 setup.py install
+ARG BUILD_DIR=/tmp/IVA
+COPY . $BUILD_DIR
+RUN cd ${BUILD_DIR} \
+ && pip3 install cython \
+ && python3 setup.py test \
+ && python3 setup.py install \
+ && rm -rf ${BUILD_DIR}

install_dependencies.sh

@@ -96,4 +96,4 @@ update_path ${mummer_dir}
 update_path ${samtools_dir}
 update_path ${smalt_dir}
 
-
+pip install cython