Commit 0553c2d9 authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

add new machines to test installation

parent fe2fe4e3
Pipeline #9569 failed with stage
in 4 minutes and 34 seconds
...@@ -7,15 +7,20 @@ RUN apt-get update &&\ ...@@ -7,15 +7,20 @@ RUN apt-get update &&\
# Install package needed # Install package needed
RUN apt-get install -y \ RUN apt-get install -y \
wget \ wget \
python3-pip
# Update pip
RUN pip3 install --upgrade pip
# Install prokka:
WORKDIR /tmp
RUN apt-get install -y\
libdatetime-perl \ libdatetime-perl \
libxml-simple-perl \ libxml-simple-perl \
libdigest-md5-perl \ libdigest-md5-perl \
git \ git \
python3-pip \
default-jre \ default-jre \
bioperl bioperl
RUN git clone https://github.com/tseemann/prokka.git
# Update pip RUN /tmp/prokka/bin/prokka --setupdb
RUN pip3 install --upgrade pip RUN ln -s /tmp/prokka/bin/prokka /usr/local/bin
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
\ No newline at end of file
from ubuntu:16.04
# Update apt-get packages
RUN apt-get update &&\
apt-get -y upgrade
# Install package needed
RUN apt-get install -y \
wget \
python3-pip
# Update pip
RUN pip3 install --upgrade pip
RUN apt-get install -y\
libdatetime-perl \
libxml-simple-perl \
libdigest-md5-perl \
git \
default-jre \
bioperl
# Install mafft 7.313
RUN rm /usr/bin/mafft # remove mafft installed with bioperl
WORKDIR /tmp
RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz &&\
tar xf mafft-7.313-with-extensions-src.tgz &&\
rm mafft-7.313-with-extensions-src.tgz
WORKDIR /tmp/mafft-7.313-with-extensions/core
RUN make clean &&\
make &&\
make install
\ No newline at end of file
from ubuntu:16.04
# Update apt-get packages
RUN apt-get update &&\
apt-get -y upgrade
# Install package needed and update pip
RUN apt-get install -y \
wget \
python3-pip
RUN pip3 install --upgrade pip
# Install mmseqs2
WORKDIR /tmp
RUN apt-get install -y cmake &&\
wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz &&\
tar xf mmseqs-static_sse41.tar.gz &&\
rm mmseqs-static_sse41.tar.gz &&\
mv /tmp/mmseqs2/bin/mmseqs /usr/local/bin &&\
# remove useless files
rm -r /tmp/mmseqs2
# Install FastME
WORKDIR /tmp
RUN apt-get install -y automake &&\
git clone https://gite.lirmm.fr/atgc/FastME.git
WORKDIR /tmp/FastME
RUN ./configure &&\
make &&\
make install
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