Remove useless images.

- 5 images are built to test installation script
- 1 image is built containing all dependencies, to use to run unit and functional tests

.gitlab-ci.yml

@@ -19,34 +19,25 @@ build-test-image:
     - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests
     - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu"
 
-# 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"
-
-# build-install-prokka:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update ; apk add git
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-prokkaonly" for_build/prokka_only
-#     - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-prokkaonly"
+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"
 
-# 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"
+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"
 
 build-ubuntu:
   only:
@@ -58,16 +49,6 @@ build-ubuntu:
     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu
     - docker push "$CI_REGISTRY_IMAGE/install-ubuntu"
 
-# build-annote_and_mafft:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update ; apk add git
-#     - git checkout master -- requirements.txt
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/annote_and_mafft
-#     - docker push "$CI_REGISTRY_IMAGE/install-annote-and-mafft"
-
 build-mafft:
   only:
     - docker
@@ -78,12 +59,12 @@ build-mafft:
     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft
     - docker push "$CI_REGISTRY_IMAGE/install-mafft"
 
-# build-mmseqs_and_fastme:
-#   only:
-#     - docker
-#   stage: build
-#   script:
-#     - apk update ; apk add git
-#     - git checkout master -- requirements.txt
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/mmseqs_and_fastme
-#     - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-and-fastme"
+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"

for_build/annote_and_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
-
-# Install prokka:
-WORKDIR /tmp
-RUN apt-get install -y\
-        libdatetime-perl \
-        libxml-simple-perl \
-        libdigest-md5-perl \
-        git \
-        default-jre \
-        bioperl
-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/prokka_only/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
-
-# Install prokka:
-WORKDIR /tmp
-RUN apt-get install -y\
-        libdatetime-perl \
-        libxml-simple-perl \
-        libdigest-md5-perl \
-        git \
-        default-jre \
-        bioperl
-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
-
-RUN rm /usr/bin/mafft  # remove mafft installed with bioperl