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Commit 84bf5588 authored by Amandine  PERRIN's avatar Amandine PERRIN
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Add sphinx installation on test machine

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Pipeline #
from ubuntu:16.04 from ubuntu:16.04
# Update apt-get packages # Update apt-get packages
RUN apt-get update &&\ RUN apt-get update &&\
apt-get -y upgrade apt-get -y upgrade
# Install package needed
# Install package needed and update pip
RUN apt-get install -y \ RUN apt-get install -y \
wget \ wget \
python3-pip \ python3-pip \
cmake # to install mmseqs cmake # to install mmseqs
# Update pip
RUN pip3 install --upgrade pip RUN pip3 install --upgrade pip
# Install barrnap # Install barrnap
WORKDIR /tmp WORKDIR /tmp
RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\ RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\
tar -xf 0.8.tar.gz &&\ tar -xf 0.8.tar.gz &&\
rm 0.8.tar.gz rm 0.8.tar.gz &&\
RUN mv /tmp/barrnap-0.8/bin/barrnap /usr/local/bin mv /tmp/barrnap-0.8/bin/barrnap /usr/local/bin &&\
# Remove heavy useless files # Remove heavy useless files
RUN rm -r /tmp/barrnap-0.8/examples /tmp/barrnap-0.8/build/*.aln rm -r /tmp/barrnap-0.8/examples /tmp/barrnap-0.8/build/*.aln
# Install prokka: # Install prokka:
WORKDIR /tmp WORKDIR /tmp
...@@ -30,17 +33,23 @@ RUN apt-get install -y\ ...@@ -30,17 +33,23 @@ RUN apt-get install -y\
libdigest-md5-perl \ libdigest-md5-perl \
git \ git \
default-jre \ default-jre \
bioperl bioperl &&\
RUN git clone https://github.com/tseemann/prokka.git git clone https://github.com/tseemann/prokka.git
RUN /tmp/prokka/bin/prokka --setupdb RUN /tmp/prokka/bin/prokka --setupdb &&\
RUN ln -s /tmp/prokka/bin/prokka /usr/local/bin ln -s /tmp/prokka/bin/prokka /usr/local/bin
# Install mmseqs2 # Install mmseqs2
WORKDIR /tmp WORKDIR /tmp
RUN wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz &&\ RUN wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz &&\
tar xf mmseqs-static_sse41.tar.gz &&\ tar xf mmseqs-static_sse41.tar.gz &&\
rm mmseqs-static_sse41.tar.gz rm mmseqs-static_sse41.tar.gz &&\
RUN mv /tmp/mmseqs2/bin/mmseqs /usr/local/bin mv /tmp/mmseqs2/bin/mmseqs /usr/local/bin &&\
# remove useless files # remove useless files
RUN rm -r /tmp/mmseqs2 rm -r /tmp/mmseqs2
# Install sphinx
RUN pip3 install sphinx &&\
pip3 install sphinx_rtd_theme
\ No newline at end of file
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