update all docker images used for tests

.gitlab-ci.yml

@@ -20,76 +20,76 @@ build-test-image:
     # - git checkout master -- requirements.txt
     - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests
     - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu"
-  tags:
-    - k8s
-
-# build-install-barrnap:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update #; apk add git
-#     # - git checkout master -- requirements.txt
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only
-#     - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly"
   # tags:
   #   - k8s
 
-# build-install-annote-and-quicktree:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update #; apk add git
-#     # - git checkout master -- requirements.txt
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree
-#     - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree"
-#   tags:
-#     - k8s
+build-install-barrnap:
+  only:
+    - docker
+  stage: build
+  script:
+    - apk update #; apk add git
+    # - git checkout master -- requirements.txt
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only
+    - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly"
+  tags:
+    - k8s
 
-# build-ubuntu:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update  # ; apk add git
-#     # - git checkout master -- requirements.txt
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu
-#     - docker push "$CI_REGISTRY_IMAGE/install-ubuntu"
-#   tags:
-#     - k8s
+build-install-annote-and-quicktree:
+  only:
+    - docker
+  stage: build
+  script:
+    - apk update #; apk add git
+    # - git checkout master -- requirements.txt
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree
+    - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree"
+  tags:
+    - k8s
 
-# build-mafft:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update # ; apk add git
-#     # - git checkout master -- requirements.txt
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft
-#     - docker push "$CI_REGISTRY_IMAGE/install-mafft"
-#   tags:
-#     - k8s
+build-ubuntu:
+  only:
+    - docker
+  stage: build
+  script:
+    - apk update  # ; apk add git
+    # - git checkout master -- requirements.txt
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu
+    - docker push "$CI_REGISTRY_IMAGE/install-ubuntu"
+  tags:
+    - k8s
 
-# build-mmseqs_and_fastme:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update # ; apk add git
-#     # - git checkout master -- requirements.txt
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme
-#     - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme"
-#   tags:
-#     - k8s
+build-mafft:
+  only:
+    - docker
+  stage: build
+  script:
+    - apk update # ; apk add git
+    # - git checkout master -- requirements.txt
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft
+    - docker push "$CI_REGISTRY_IMAGE/install-mafft"
+  tags:
+    - k8s
 
-# build-install-prodigal:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal
-#     - docker push "$CI_REGISTRY_IMAGE/install-prodigal"
-#   tags:
-#     - k8s
+build-mmseqs_and_fastme:
+  only:
+    - docker
+  stage: build
+  script:
+    - apk update # ; apk add git
+    # - git checkout master -- requirements.txt
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme
+    - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme"
+  tags:
+    - k8s
+
+build-install-prodigal:
+  only:
+    - docker
+  stage: build
+  script:
+    - apk update
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal
+    - docker push "$CI_REGISTRY_IMAGE/install-prodigal"
+  tags:
+    - k8s

for_build/annote_and_1tree/Dockerfile

-from ubuntu:18.04
+from ubuntu:20.04
 
 # Update apt-get packages
 RUN apt-get update &&\
@@ -13,30 +13,31 @@ RUN apt-get install -y \
 RUN pip3 install --upgrade pip
 
 # Update makeblastdb and blastp for prokka
-WORKDIR /tmp
-RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
+WORKDIR /install_dir
+RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
     tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
-    cp /tmp/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
-    cp /tmp/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
+    cp /install_dir/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
+    cp /install_dir/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
     rm ncbi-blast-2.10.1+-x64-linux.tar.gz
 
+
 # Install prokka:
-WORKDIR /tmp
-RUN apt-get install -y\
+WORKDIR /install_dir
+RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
         libdatetime-perl \
         libxml-simple-perl \
         libdigest-md5-perl \
         git \
         default-jre \
-        bioperl &&\
-    git clone https://github.com/tseemann/prokka.git &&\
-    /tmp/prokka/bin/prokka --setupdb &&\
-    ln -s /tmp/prokka/bin/prokka /usr/local/bin
-RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
+        bioperl
+RUN git clone https://github.com/tseemann/prokka.git
+RUN /install_dir/prokka/bin/prokka --setupdb &&\
+    ln -s /install_dir/prokka/bin/prokka /usr/local/bin
+
 
 # Install quicktree
-WORKDIR /tmp
+WORKDIR /install_dir
 RUN git clone https://github.com/tseemann/quicktree
-WORKDIR quicktree
+WORKDIR /install_dir/quicktree
 RUN make &&\
-    ln -s /tmp/quicktree/quicktree /usr/local/bin
+    ln -s /install_dir/quicktree/quicktree /usr/local/bin

for_build/barrnap_only/Dockerfile

-from ubuntu:18.04
+from ubuntu:20.04
 
 # Update apt-get packages
 RUN apt-get update &&\
@@ -18,12 +18,14 @@ RUN apt-get install -y \
 
 RUN pip3 install --upgrade pip
 
-
 # Install barrnap
-WORKDIR /tmp
+WORKDIR /install_dir
 RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\
     tar -xf 0.8.tar.gz &&\
-    rm 0.8.tar.gz
-RUN ln -s /tmp/barrnap-0.8/bin/barrnap /usr/local/bin
+    rm 0.8.tar.gz &&\
+    mv /install_dir/barrnap-0.8/bin/barrnap /usr/local/bin  &&\
+    # Remove heavy useless files
+    rm -r /install_dir/barrnap-0.8/examples /install_dir/barrnap-0.8/build/*.aln
+
 
 RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
\ No newline at end of file

for_build/mafft/Dockerfile

-from ubuntu:18.04
+from ubuntu:20.04
 
 # Update apt-get packages
 RUN apt-get update &&\
@@ -25,11 +25,11 @@ RUN apt-get install -y \
 
 # Install mafft 7.313
 RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
-WORKDIR /tmp
+WORKDIR /install_dir
 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
+WORKDIR /install_dir/mafft-7.313-with-extensions/core
 RUN make clean &&\
     make &&\
     make install

for_build/mmseqs_and_fastme/Dockerfile

-from ubuntu:18.04
+from ubuntu:20.04
 
 
 # Update apt-get packages
@@ -16,21 +16,21 @@ RUN apt-get install -y \
 RUN pip3 install --upgrade pip
 
 
-# Install MMseqs2 (Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e ?)
-WORKDIR /tmp
+# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
+WORKDIR /install_dir
 RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
     tar xvfz mmseqs-linux-sse41.tar.gz &&\
     rm mmseqs-linux-sse41.tar.gz &&\
-    mv /tmp/mmseqs/bin/mmseqs /usr/local/bin &&\
+    mv /install_dir/mmseqs/bin/mmseqs /usr/local/bin &&\
     # remove useless files
-    rm -r /tmp/mmseqs
+    rm -r /install_dir/mmseqs
 
 
-# Install FastME
-WORKDIR /tmp
+# Install FastME FastME 2.1.6.1
+WORKDIR /install_dir
 RUN apt-get install -y automake  &&\
     git clone https://gite.lirmm.fr/atgc/FastME.git
-WORKDIR /tmp/FastME
-RUN ./configure &&\
-    make &&\
-    make install
+WORKDIR /install_dir/FastME/tarball
+RUN tar xzf fastme-2.1.6.2.tar.gz &&\
+    rm fastme-2.1.6.2.tar.gz &&\
+    ln -s /install_dir/FastME/tarball/fastme-2.1.6.2/binaries/fastme-2.1.6.2-linux64-omp /usr/local/bin/fastme

for_build/prodigal/Dockerfile

-from ubuntu:18.04
+from ubuntu:20.04
 
 # Update apt-get packages
 RUN apt-get update &&\
@@ -14,8 +14,12 @@ RUN apt-get install -y \
 # Upgrade pip
 RUN pip3 install --upgrade pip
 
+
 # Install prodigal
-RUN apt-get install zlib1g-dev &&\
-    git clone https://github.com/hyattpd/Prodigal.git
-WORKDIR Prodigal
-RUN make install
+WORKDIR /install_dir
+RUN wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz &&\
+    tar -xzf v2.6.3.tar.gz &&\
+    rm v2.6.3.tar.gz
+WORKDIR /install_dir/Prodigal-2.6.3
+RUN make &&\
+    make install
\ No newline at end of file

for_build/ubuntu/Dockerfile

-from ubuntu:18.04
+from ubuntu:20.04
 
 # Update apt-get packages
 RUN apt-get update &&\

for_tests/Dockerfile

@@ -96,7 +96,7 @@ RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
     ln -s /install_dir/FastTreeMP /usr/local/bin
 
 
-## Install FastME FastME 2.1.6.1
+# Install FastME FastME 2.1.6.1
 WORKDIR /install_dir
 RUN apt-get install -y automake  &&\
     git clone https://gite.lirmm.fr/atgc/FastME.git