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from comics/augustus:3.2.2 LABEL maintainer "erik.kastman@gmail.com" ENV APP_NAME=busco ARG BUSCO_VERSION=3.0.0 ENV BUSCO_VERSION_SHORTHASH=2f3dd7b4 ENV APP_PATH=/software/applications ENV DEST=$APP_PATH/$APP_NAME/ ENV PATH=$DEST/$BUSCO_VERSION/scripts:$PATH ENV BLAST_VERSION=2.2.31 RUN yum install -y \ python \ emboss \ git \ perl-Archive-Tar \ perl-List-MoreUtils \ perl-Digest-MD5 \ && yum clean all; RUN rpm -ivh ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/$BLAST_VERSION/ncbi-blast-${BLAST_VERSION}+-2.x86_64.rpm RUN cd $APP_PATH; \ wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz && \ tar -xzf hmmer-3.1b2-linux-intel-x86_64.tar.gz && \ rm hmmer-3.1b2-linux-intel-x86_64.tar.gz # n.b. Downloading with Git is *not* preferred by Docker developers, # but BUSCO distributes using gitlab which does not provide automatic zips # of tags, so this seems to be the cleanest way to grab versions from upstream. RUN git clone https://gitlab.com/ezlab/busco.git $DEST/$BUSCO_VERSION && \ cd $DEST/$BUSCO_VERSION && \ git checkout $BUSCO_VERSION_SHORTHASH && \ python setup.py install WORKDIR $DEST/$BUSCO_VERSION COPY config.ini $DEST/$BUSCO_VERSION/config ENTRYPOINT ["/software/applications/busco/3.0.0/scripts/run_BUSCO.py"] CMD ["-h"]
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