Merge pull request #165 from pbelmann/feature/prokka_docker_image

Feature/prokka docker image

docker/toolkit-prokka/Dockerfile

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+FROM ubuntu:18.04
+
+# metadata
+LABEL website="https://github.com/tseemann/prokka"
+LABEL license="https://github.com/tseemann/prokka#licence"
+
+# install dependencies
+RUN apt-get update && \
+    apt-get -y --no-install-recommends install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl hmmer wget \
+                       zlib1g-dev python liblzma-dev libbz2-dev xz-utils curl g++ make \
+                       less bzip2 gzip libidn11-dev &&\ 
+    apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+#get Bioperl
+#RUN cpan Bio::Perl
+
+# install bedtools 2.29.0 since >=2.27.0 is required for barrnap and the apt-get package is 2.25.0
+# dependencies required for bedtools: zlib1g-dev python liblzma-dev libbz2-dev xz-utils curl g++
+RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz && \
+  tar -zxf bedtools-2.29.0.tar.gz && \
+  rm bedtools-2.29.0.tar.gz && \
+  cd bedtools2 && \
+  make
+
+# add bedtools to PATH for barrnap test
+ENV PATH="$PATH:/bedtools2/bin"
+
+# install barrnap
+RUN wget https://github.com/tseemann/barrnap/archive/0.9.tar.gz &&\
+    tar -zxf 0.9.tar.gz &&\
+    rm 0.9.tar.gz &&\
+    cd barrnap-0.9 &&\
+    make test
+
+#get prokka
+RUN git clone https://github.com/tseemann/prokka && \
+    cd prokka && \
+    git fetch origin pull/219/head:partialgenes && \
+    git checkout partialgenes
+
+# install tbl2asn manually since the one included with prokka is expired.
+RUN wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz -O linux64.tbl2asn.gz && \
+    gunzip linux64.tbl2asn.gz && \
+    mv linux64.tbl2asn /usr/bin/tbl2asn && \
+    chmod 755 /usr/bin/tbl2asn
+
+# put prokka in PATH & 
+# set PATH to prioritize /usr/bin/tbl2asn before /prokka/binaries/tbl2asn
+ENV PATH="$PATH:/prokka/bin"
+
+#setupdb
+RUN prokka --setupdb
+
+WORKDIR /data
+

docker/toolkit-prokka/VERSION

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+1.12.0-0