test installation of docker image for tests

.gitlab-ci.yml

@@ -22,73 +22,73 @@ 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

@@ -5,15 +5,22 @@ RUN apt-get update &&\
     apt-get -y upgrade
 
 
-# Install package needed and update pip
+# Install packages needed and update pip
 RUN apt-get install -y \
         wget \
         python3-pip \
         python3
-
 RUN pip3 install --upgrade pip
 
 
+# Update makeblastdb
+WORKDIR /tmp
+RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.9.0+-x64-linux.tar.gz &&\
+    tar zxvpf ncbi-blast-2.9.0+-x64-linux.tar.gz &&\
+    cp /tmp/ncbi-blast-2.9.0+/bin/makeblastdb /usr/local/bin/ &&\
+    rm ncbi-blast-2.9.0+-x64-linux.tar.gz
+
+
 # Install mash
 WORKDIR /tmp
 RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
@@ -41,21 +48,20 @@ RUN apt-get install -y\
         libdigest-md5-perl \
         git \
         default-jre \
-        bioperl &&\
-    git clone https://github.com/tseemann/prokka.git
+        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
 
 
-# Install mmseqs2
+# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
 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 &&\
+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/mmseqs2/bin/mmseqs /usr/local/bin &&\
     # remove useless files
-    rm -r /tmp/mmseqs2
+    rm -r /tmp/mmseqs
 
 
 # Install mafft 7.313
@@ -70,26 +76,27 @@ RUN make clean &&\
     make install
 
 
-# Install FastTree
-WORKDIR /tmp
-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
-
-
-# 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
-
-
-# Install quicktree
-WORKDIR /tmp
-RUN git clone https://github.com/tseemann/quicktree
-WORKDIR quicktree
-RUN make &&\
-    ln -s /tmp/quicktree/quicktree /usr/local/bin
+## Install FastTree
+#WORKDIR /tmp
+#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/FastTre#eMP /usr/local/bin#
+#
+#
+## 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
+#
+#
+## Install quicktree
+#WORKDIR /tmp
+#RUN git clone https://github.com/tseemann/quicktree
+#WORKDIR quicktree
+#RUN make &&\
+#    ln -s /tmp/quicktree/quicktree /usr/local/bin
+#
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