add new machines to test installation

for_build/basics/Dockerfile → for_build/annote_and_mafft/Dockerfile

@@ -7,15 +7,20 @@ RUN apt-get update &&\
 # Install package needed
 RUN apt-get install -y \
         wget \
+        python3-pip
+
+# Update pip
+RUN pip3 install --upgrade pip
+
+# Install prokka:
+WORKDIR /tmp
+RUN apt-get install -y\
         libdatetime-perl \
         libxml-simple-perl \
         libdigest-md5-perl \
         git \
-        python3-pip \
         default-jre \
         bioperl
-
-# Update pip
-RUN pip3 install --upgrade pip
-
-RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
\ No newline at end of file
+RUN git clone https://github.com/tseemann/prokka.git
+RUN /tmp/prokka/bin/prokka --setupdb
+RUN ln -s /tmp/prokka/bin/prokka /usr/local/bin

for_build/mafft/Dockerfile

+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

for_build/mmseqs_and_fastme/Dockerfile

+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