diff --git a/roary/3.13.0/Dockerfile b/roary/3.13.0/Dockerfile index 2bde139cc..1bc45c083 100644 --- a/roary/3.13.0/Dockerfile +++ b/roary/3.13.0/Dockerfile @@ -2,7 +2,7 @@ FROM ubuntu:focal # metadata LABEL base.image="ubuntu:focal" -LABEL dockerfile.version="1" +LABEL dockerfile.version="2" LABEL software="Roary" LABEL software.version="3.13.0" LABEL description="Rapid large-scale prokaryotic pan genome analysis" @@ -15,11 +15,38 @@ LABEL maintainer.email="kapsakcj@gmail.com" ARG DEBIAN_FRONTEND=noninteractive # install roary 3.13.0 via apt; cleanup apt garbage; make /data and /kraken_db -RUN apt-get update && apt-get install -y --no-install-recommends roary && \ +RUN apt-get update && apt-get install -y --no-install-recommends roary \ + wget \ + zlib1g-dev \ + make \ + g++ \ + rsync \ + cpanminus && \ apt-get autoclean && \ rm -rf /var/lib/apt/lists/* && \ mkdir /data /kraken_db +# this perl module and rsync required for kraken-build +RUN cpanm --force --notest Getopt::Std + +# DL Jellyfish, unpack, and install +RUN wget https://github.com/gmarcais/Jellyfish/releases/download/v1.1.12/jellyfish-1.1.12.tar.gz && \ + tar -zxf jellyfish-1.1.12.tar.gz && \ + rm -rf jellyfish-1.1.12.tar.gz && \ + cd jellyfish-1.1.12 && \ + ./configure --prefix=/opt/ && \ + make -j 4 && \ + make install + +# DL Kraken v1.1.1, unpack, and install +RUN wget https://github.com/DerrickWood/kraken/archive/v1.1.1.tar.gz && \ + tar -xzf v1.1.1.tar.gz && \ + rm -rf v1.1.1.tar.gz && \ + cd kraken-1.1.1 && \ + mkdir /opt/kraken && \ + ./install_kraken.sh /opt/kraken/ + WORKDIR /data -# set perl locale settings -ENV LC_ALL=C +# set perl locale settings and PATH +ENV LC_ALL=C.UTF-8 \ + PATH="$PATH:/opt/kraken:/opt/bin"