new version of docker image for tests:

- prokka with updated tbl2asn binary
- use ubuntu 20.04

.gitlab-ci.yml

@@ -23,73 +23,73 @@ build-test-image:
   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-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-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-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-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-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-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-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-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
+# 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_tests/Dockerfile

-from ubuntu:18.04
+from ubuntu:20.04
 
 # Update apt-get packages
 RUN apt-get update &&\
@@ -12,47 +12,50 @@ RUN apt-get install -y \
         python3-pip
 # Upgrade pip
 RUN pip3 install --upgrade pip
+RUN mkdir /install_dir
 
 
 # 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 mash
-WORKDIR /tmp
+WORKDIR /install_dir
 RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
     tar -xf mash-Linux64-v2.2.tar &&\
     rm mash-Linux64-v2.2.tar &&\
-    mv /tmp/mash-Linux64-v2.2/mash /usr/local/bin &&\
+    mv /install_dir/mash-Linux64-v2.2/mash /usr/local/bin &&\
     rm -r mash-Linux64-v2.2
 
 
 # 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 &&\
-    mv /tmp/barrnap-0.8/bin/barrnap /usr/local/bin  &&\
+    mv /install_dir/barrnap-0.8/bin/barrnap /usr/local/bin  &&\
     # Remove heavy useless files
-    rm -r /tmp/barrnap-0.8/examples /tmp/barrnap-0.8/build/*.aln
+    rm -r /install_dir/barrnap-0.8/examples /install_dir/barrnap-0.8/build/*.aln
+
 
 # Install prodigal
-WORKDIR /tmp
+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 /tmp/Prodigal-2.6.3
+WORKDIR /install_dir/Prodigal-2.6.3
 RUN make &&\
     make install
 
+
 # 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 \
@@ -60,68 +63,68 @@ RUN apt-get install -y\
         default-jre \
         bioperl
 RUN git clone https://github.com/tseemann/prokka.git
-RUN /tmp/prokka/bin/prokka --setupdb &&\
-    ln -s /tmp/prokka/bin/prokka /usr/local/bin
+RUN /install_dir/prokka/bin/prokka --setupdb &&\
+    ln -s /install_dir/prokka/bin/prokka /usr/local/bin
 
 
 # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
-WORKDIR /tmp
+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 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
 
 
 # Install FastTree version 2.1.11 Double precision (No SSE3)
-WORKDIR /tmp
+WORKDIR /install_dir
 RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
     gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\
-    ln -s /tmp/FastTreeMP /usr/local/bin
+    ln -s /install_dir/FastTreeMP /usr/local/bin
 
 
 ## Install FastME FastME 2.1.6.1
-WORKDIR /tmp
+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
 
 
 # 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
 
 
 # Install iqtree
-WORKDIR /tmp
+WORKDIR /install_dir
 RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
 RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\
     rm iqtree-1.6.12-Linux.tar.gz &&\
-    ln -s /tmp/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
+    ln -s /install_dir/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
 
 
 # Install iqtree2
-WORKDIR /tmp
+WORKDIR /install_dir
 RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
 RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
     rm iqtree-2.0.6-Linux.tar.gz &&\
-    ln -s /tmp/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin
+    ln -s /install_dir/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin