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added kraken 1.1.1 to roary 3.13.0 dockerfile #260

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Jan 21, 2022
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added kraken 1.1.1 to roary 3.13.0 dockerfile #260

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35 changes: 31 additions & 4 deletions roary/3.13.0/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -15,11 +15,38 @@ LABEL maintainer.email="[email protected]"
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"